N E X T F L O W ~ version 21.04.1 Launching `nf-core/sarek` [clever_euler] - revision: 68b9930a74 [master] WARN: It appears you have never run this project before -- Option `-resume` is ignored ------------------------------------------------------ ,--./,-. ___ __ __ __ ___ /,-._.--~' |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' ____ .´ _ `. / |\`-_ \ __ __ ___ | | \ `-| |__` /\ |__) |__ |__/ \ | \ / .__| /¯¯\ | \ |___ | \ `|____\´ nf-core/sarek v2.7.1 ------------------------------------------------------ WARN: Found unexpected parameters: * --saveReference: true - Ignore this warning: params.schema_ignore_params = "saveReference" Core Nextflow options revision : master runName : clever_euler containerEngine : singularity container : nfcore/sarek:2.7.1 launchDir : /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples workDir : /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work projectDir : /home/sigenae/.nextflow/assets/nf-core/sarek userName : sigenae profile : standard configFiles : /home/sigenae/.nextflow/assets/nf-core/sarek/nextflow.config, /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/./genotoul_1.config Input/output options input : /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/input.tsv Main options tools : HaplotypeCaller,FreeBayes,mpileup skip_qc : null Trim/split FASTQ clip_r1 : 0 clip_r2 : 0 three_prime_clip_r1 : 0 three_prime_clip_r2 : 0 trim_nextseq : 0 Preprocessing markdup_java_options : "-Xms4000m -Xmx7g" Variant Calling ascat_ploidy : null ascat_purity : null cf_contamination : null cf_ploidy : 2 generate_gvcf : true read_structure1 : null read_structure2 : null Annotation annotate_tools : null cadd_indels : false cadd_indels_tbi : false cadd_wg_snvs : false cadd_wg_snvs_tbi : false snpeff_cache : null vep_cache : null Reference genome options genome : Gallus_gallus-5.0 bwa : /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/Data//Gallus_gallus.Gallus_gallus-5.0.dna.toplevel.fa.{amb,ann,bwt,pac,sa} dict : /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/Data//Gallus_gallus.Gallus_gallus-5.0.dna.toplevel.dict fasta : /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/Data//Gallus_gallus.Gallus_gallus-5.0.dna.toplevel.fa known_indels : /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/Data//Gallus_gallus_incl_consequences.vcf known_indels_index : /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/Data//Gallus_gallus_incl_consequences.vcf.idx igenomes_base : s3://ngi-igenomes/igenomes/ genomes_base : /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/Data/ Generic options max_multiqc_email_size : 25 MB sequencing_center : null Max job request options single_cpu_mem : 7 GB max_cpus : 10 max_memory : 120 GB max_time : 4d Institutional config options config_profile_description: The Genotoul cluster profile config_profile_contact : support.bioinfo.genotoul@inra.fr config_profile_url : http://bioinfo.genotoul.fr/ ------------------------------------------------------ Only displaying parameters that differ from defaults. ------------------------------------------------------ Pipeline Release : master Run Name : clever_euler Max Resources : 120 GB memory, 10 cpus, 4d time per job Container : singularity - nfcore/sarek:2.7.1 Output dir : ./results Launch dir : /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples Working dir : /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work Script dir : /home/sigenae/.nextflow/assets/nf-core/sarek User : sigenae Input : /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/input.tsv Step : mapping Genome : Gallus_gallus-5.0 Nucleotides/s : 1000 Tools : haplotypecaller, freebayes, mpileup MarkDuplicates : Options Java options : "-Xms4000m -Xmx7g" GATK Spark : No Save BAMs mapped : No Skip MarkDuplicates: No GVCF : Yes AWS iGenomes base : s3://ngi-igenomes/igenomes/ Genomes base : /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/Data/ Save Reference : No BWA indexes : /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/Data//Gallus_gallus.Gallus_gallus-5.0.dna.toplevel.fa.{amb,ann,bwt,pac,sa} dict : /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/Data//Gallus_gallus.Gallus_gallus-5.0.dna.toplevel.dict fasta reference : /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/Data//Gallus_gallus.Gallus_gallus-5.0.dna.toplevel.fa known indels : /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/Data//Gallus_gallus_incl_consequences.vcf known indels index: /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/Data//Gallus_gallus_incl_consequences.vcf.idx Publish dir mode : copy Config Profile : standard Config Description: The Genotoul cluster profile Config Contact : support.bioinfo.genotoul@inra.fr Config URL : http://bioinfo.genotoul.fr/ Config Files : /home/sigenae/.nextflow/assets/nf-core/sarek/nextflow.config, /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/./genotoul_1.config ---------------------------------------------------- [- ] process > get_software_versions - [- ] process > get_software_versions - [- ] process > BuildBWAindexes - [- ] process > get_software_versions - [- ] process > BuildBWAindexes - [- ] process > BuildDict - [- ] process > get_software_versions - [- ] process > BuildBWAindexes - [- ] process > BuildDict - [- ] process > BuildFastaFai - [- ] process > get_software_versions - [- ] process > BuildBWAindexes - [- ] process > BuildDict - [- ] process > BuildFastaFai - [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > get_software_versions - [- ] process > BuildBWAindexes - [- ] process > BuildDict - [- ] process > BuildFastaFai - [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > get_software_versions - [- ] process > BuildBWAindexes - [- ] process > BuildDict - [- ] process > BuildFastaFai - [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > get_software_versions - [- ] process > BuildBWAindexes - [- ] process > BuildDict - [- ] process > BuildFastaFai - [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > get_software_versions - [- ] process > BuildBWAindexes - [- ] process > BuildDict - [- ] process > BuildFastaFai - [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > get_software_versions - [- ] process > BuildBWAindexes - [- ] process > BuildDict - [- ] process > BuildFastaFai - [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [- ] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [- ] process > BuildFastaFai [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [- ] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [- ] process > BuildFastaFai [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [- ] process > FastQCFQ [ 0%] 0 of 1 [- ] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [- ] process > FastQCFQ [ 0%] 0 of 2 [- ] process > FastQCBAM - executor > slurm (1) [- ] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [- ] process > FastQCFQ [ 0%] 0 of 2 [- ] process > FastQCBAM - executor > slurm (2) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [- ] process > FastQCFQ [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - executor > slurm (2) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [- ] process > FastQCFQ [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - executor > slurm (3) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - executor > slurm (3) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - executor > slurm (4) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [- ] process > Output_documentation [ 0%] 0 of 1 executor > slurm (5) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [ 0%] 0 of 1 executor > slurm (5) [bf/ce6cce] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (5) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals [ 0%] 0 of 1 [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (6) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [ 0%] 0 of 1 [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads [ 0%] 0 of 2 [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (8) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [ 0%] 0 of 1 [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (8) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [- ] process > CreateIntervalBeds - [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (9) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [ 0%] 0 of 1 [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (9) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [ 0%] 0 of 1 [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (9) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (9) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [e3/c164d0] process > FastQCFQ (F_Aln-SNP-1) [ 50%] 1 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (9) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (9) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [32/b505ae] process > MapReads (F_Aln-SNP-1) [ 50%] 1 of 2 [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC [ 0%] 0 of 1 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (10) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [32/b505ae] process > MapReads (F_Aln-SNP-1) [ 50%] 1 of 2 [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [b6/9f2e36] process > BamQC (F_Aln-SNP-SRR7062654_1) [ 0%] 0 of 1 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (10) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [32/b505ae] process > MapReads (F_Aln-SNP-1) [ 50%] 1 of 2 [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [b6/9f2e36] process > BamQC (F_Aln-SNP-SRR7062654_1) [ 0%] 0 of 1 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (10) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [b6/9f2e36] process > BamQC (F_Aln-SNP-SRR7062654_1) [ 0%] 0 of 1 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (13) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [ 0%] 0 of 2 [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 0%] 0 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (13) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [ 0%] 0 of 2 [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 0%] 0 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (13) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [ 0%] 0 of 2 [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [b6/9f2e36] process > BamQC (F_Aln-SNP-SRR7062654_1) [ 50%] 1 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (13) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [ 0%] 0 of 2 [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (13) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (13) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator [ 0%] 0 of 16 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (13) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator [ 0%] 0 of 24 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (13) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator [ 0%] 0 of 85 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (13) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator [ 0%] 0 of 110 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (13) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator [ 0%] 0 of 143 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (14) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [9f/327787] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 335 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (14) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [9f/327787] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 364 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (15) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [18/8853c9] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (17) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [3d/0bcf1b] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (19) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [d1/21183a] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (20) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [a2/1a9980] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (22) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [ac/b2d41c] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (24) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [00/cfe02e] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (26) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [6e/791142] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (29) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [e7/bfcf5a] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (31) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [0b/361861] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (34) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [d1/ed6a6c] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (36) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [64/afe193] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (38) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [03/180f3c] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (40) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [dd/2e9738] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (43) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [96/0453af] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (47) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [62/4d1313] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (50) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [77/b00e28] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (53) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [c7/900ed2] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (55) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [71/f86b53] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (58) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [1c/fe0e78] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (61) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [7b/d94c42] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (64) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [45/8e3629] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (68) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [5f/4c438a] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (72) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [9d/820e2d] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (76) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [2b/8ca952] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (79) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [52/3c7b1d] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (82) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [ac/cd5815] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (85) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [04/c3f79a] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (88) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [48/d7df53] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (92) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [f9/99ac63] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (96) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [3e/c83f09] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (101) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [a5/7b95b8] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (105) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [fe/7b5f1a] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (109) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [52/b31ffa] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (112) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [1f/98cb74] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (112) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [1f/98cb74] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (112) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [1f/98cb74] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (112) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [1f/98cb74] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (112) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [1f/98cb74] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (113) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [57/96f40f] process > BaseRecalibrator (F_Aln-SNP... [ 1%] 3 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (116) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [30/d2cdf1] process > BaseRecalibrator (F_Aln-SNP... [ 1%] 4 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (116) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [ee/fa0206] process > BaseRecalibrator (F_Aln-SNP... [ 2%] 7 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (118) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [52/b31ffa] process > BaseRecalibrator (F_Aln-SNP... [ 5%] 17 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (121) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [40/1824c6] process > BaseRecalibrator (F_Aln-SNP... [ 5%] 18 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (123) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [3c/81e73a] process > BaseRecalibrator (F_Aln-SNP... [ 5%] 18 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (127) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [06/b368a4] process > BaseRecalibrator (F_Aln-SNP... [ 5%] 18 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (130) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [2b/d72244] process > BaseRecalibrator (F_Aln-SNP... [ 5%] 18 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (130) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [01/2903bf] process > BaseRecalibrator (F_Aln-SNP... [ 6%] 24 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (131) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [68/4f6b0d] process > BaseRecalibrator (F_Aln-SNP... [ 9%] 33 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (132) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [7f/2decc7] process > BaseRecalibrator (F_Aln-SNP... [ 10%] 37 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (133) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [5b/570c3d] process > BaseRecalibrator (F_Aln-SNP... [ 11%] 40 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (134) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [1f/38dd34] process > BaseRecalibrator (F_Aln-SNP... [ 11%] 40 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (135) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [60/2c1ba5] process > BaseRecalibrator (F_Aln-SNP... [ 11%] 40 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (136) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [c0/d08cbf] process > BaseRecalibrator (F_Aln-SNP... [ 11%] 40 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (137) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [77/69c9a7] process > BaseRecalibrator (F_Aln-SNP... [ 11%] 40 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (138) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [2c/6dd0bf] process > BaseRecalibrator (F_Aln-SNP... [ 11%] 40 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (140) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [36/06abd4] process > BaseRecalibrator (F_Aln-SNP... [ 11%] 40 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (141) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [04/a892d4] process > BaseRecalibrator (F_Aln-SNP... [ 11%] 40 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (142) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [76/6ab1c0] process > BaseRecalibrator (F_Aln-SNP... [ 11%] 40 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (144) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [02/ecdadb] process > BaseRecalibrator (F_Aln-SNP... [ 11%] 40 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (145) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [ae/95acac] process > BaseRecalibrator (F_Aln-SNP... [ 11%] 40 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (146) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [be/0010e4] process > BaseRecalibrator (F_Aln-SNP... [ 11%] 40 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (148) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [7d/d3f476] process > BaseRecalibrator (F_Aln-SNP... [ 11%] 40 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (149) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [25/7d9255] process > BaseRecalibrator (F_Aln-SNP... [ 11%] 40 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (151) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [ae/295d8d] process > BaseRecalibrator (F_Aln-SNP... [ 11%] 40 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (152) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [80/cbd1a2] process > BaseRecalibrator (F_Aln-SNP... [ 11%] 40 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (152) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [00/cfe02e] process > BaseRecalibrator (F_Aln-SNP... [ 11%] 41 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (153) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [04/c3f79a] process > BaseRecalibrator (F_Aln-SNP... [ 14%] 51 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (153) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [24/f59281] process > BaseRecalibrator (F_Aln-SNP... [ 15%] 56 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (154) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [d8/a92fa5] process > BaseRecalibrator (F_Aln-SNP... [ 16%] 61 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (155) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [bc/a83396] process > BaseRecalibrator (F_Aln-SNP... [ 17%] 63 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (156) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [6e/e3ddb9] process > BaseRecalibrator (F_Aln-SNP... [ 17%] 63 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (157) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [eb/b8eb3d] process > BaseRecalibrator (F_Aln-SNP... [ 17%] 63 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (159) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [10/31f5bc] process > BaseRecalibrator (F_Aln-SNP... [ 17%] 63 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (160) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [a6/12528c] process > BaseRecalibrator (F_Aln-SNP... [ 17%] 63 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (162) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [c3/b0f0c1] process > BaseRecalibrator (F_Aln-SNP... [ 17%] 63 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (164) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [ba/87efe9] process > BaseRecalibrator (F_Aln-SNP... [ 17%] 63 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (166) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [87/970000] process > BaseRecalibrator (F_Aln-SNP... [ 17%] 63 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (167) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [7e/db192d] process > BaseRecalibrator (F_Aln-SNP... [ 17%] 63 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (169) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [65/d50411] process > BaseRecalibrator (F_Aln-SNP... [ 17%] 63 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (171) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [0d/1705bb] process > BaseRecalibrator (F_Aln-SNP... [ 17%] 63 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (173) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [9b/2570a2] process > BaseRecalibrator (F_Aln-SNP... [ 17%] 63 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (175) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [02/81b5bd] process > BaseRecalibrator (F_Aln-SNP... [ 17%] 63 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (175) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [6e/791142] process > BaseRecalibrator (F_Aln-SNP... [ 17%] 64 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (180) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [76/3f2df0] process > BaseRecalibrator (F_Aln-SNP... [ 18%] 68 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (180) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [67/607d91] process > BaseRecalibrator (F_Aln-SNP... [ 19%] 71 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (183) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [1e/b09453] process > BaseRecalibrator (F_Aln-SNP... [ 19%] 71 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (183) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [12/c72cd3] process > BaseRecalibrator (F_Aln-SNP... [ 20%] 75 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (188) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [4b/de4a9e] process > BaseRecalibrator (F_Aln-SNP... [ 21%] 77 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (189) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [6d/9fd34c] process > BaseRecalibrator (F_Aln-SNP... [ 21%] 77 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (190) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [2b/d72244] process > BaseRecalibrator (F_Aln-SNP... [ 23%] 85 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (196) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [8c/9f603f] process > BaseRecalibrator (F_Aln-SNP... [ 23%] 85 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (197) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [a8/22cf48] process > BaseRecalibrator (F_Aln-SNP... [ 23%] 85 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (198) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [77/69c9a7] process > BaseRecalibrator (F_Aln-SNP... [ 25%] 94 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (202) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [aa/bbd900] process > BaseRecalibrator (F_Aln-SNP... [ 26%] 97 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (208) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [4a/c8b8cb] process > BaseRecalibrator (F_Aln-SNP... [ 26%] 97 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (209) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [c7/1597a6] process > BaseRecalibrator (F_Aln-SNP... [ 26%] 97 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (212) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [e7/39c72c] process > BaseRecalibrator (F_Aln-SNP... [ 27%] 100 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (212) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [e7/39c72c] process > BaseRecalibrator (F_Aln-SNP... [ 27%] 100 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (212) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [e7/39c72c] process > BaseRecalibrator (F_Aln-SNP... [ 27%] 100 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (212) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [e7/39c72c] process > BaseRecalibrator (F_Aln-SNP... [ 27%] 100 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (212) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [5b/570c3d] process > BaseRecalibrator (F_Aln-SNP... [ 28%] 102 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (216) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [2e/788d1e] process > BaseRecalibrator (F_Aln-SNP... [ 30%] 112 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (221) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [26/75e60a] process > BaseRecalibrator (F_Aln-SNP... [ 31%] 113 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (225) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [4d/a4047e] process > BaseRecalibrator (F_Aln-SNP... [ 31%] 113 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (226) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [ae/18896c] process > BaseRecalibrator (F_Aln-SNP... [ 32%] 117 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (231) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [b1/26a73e] process > BaseRecalibrator (F_Aln-SNP... [ 34%] 124 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (236) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [9b/8f6094] process > BaseRecalibrator (F_Aln-SNP... [ 34%] 124 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (237) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [b3/0d752f] process > BaseRecalibrator (F_Aln-SNP... [ 35%] 130 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (240) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [63/18038c] process > BaseRecalibrator (F_Aln-SNP... [ 40%] 147 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (244) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [1c/67fc57] process > BaseRecalibrator (F_Aln-SNP... [ 40%] 147 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (249) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [ff/31d190] process > BaseRecalibrator (F_Aln-SNP... [ 40%] 147 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (254) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [d2/bf26d5] process > BaseRecalibrator (F_Aln-SNP... [ 40%] 147 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (258) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [ba/34fdde] process > BaseRecalibrator (F_Aln-SNP... [ 40%] 147 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (259) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [7f/c04cd2] process > BaseRecalibrator (F_Aln-SNP... [ 40%] 147 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (261) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [9b/a3e06c] process > BaseRecalibrator (F_Aln-SNP... [ 45%] 165 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (264) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [60/1b9a31] process > BaseRecalibrator (F_Aln-SNP... [ 47%] 173 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (266) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [63/cd6ab9] process > BaseRecalibrator (F_Aln-SNP... [ 47%] 173 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (269) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [73/a285b4] process > BaseRecalibrator (F_Aln-SNP... [ 47%] 173 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (273) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [44/b4c9b2] process > BaseRecalibrator (F_Aln-SNP... [ 47%] 173 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (279) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [81/4ee155] process > BaseRecalibrator (F_Aln-SNP... [ 47%] 173 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (285) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [18/6beef3] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [1b/ebc8f1] process > BaseRecalibrator (F_Aln-SNP... [ 47%] 173 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (285) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 [- ] process > Sentieon_Dedup - [f1/a35890] process > BaseRecalibrator (F_Aln-SNP... [ 47%] 174 of 370 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (287) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [c6/a02d81] process > BaseRecalibrator (F_Aln-SNP... [ 46%] 175 of 378 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (287) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [c6/a02d81] process > BaseRecalibrator (F_Aln-SNP... [ 46%] 175 of 380 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (287) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [c6/a02d81] process > BaseRecalibrator (F_Aln-SNP... [ 45%] 175 of 386 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (288) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [0b/0857e3] process > BaseRecalibrator (F_Aln-SNP... [ 45%] 175 of 393 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (288) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [0b/0857e3] process > BaseRecalibrator (F_Aln-SNP... [ 43%] 175 of 405 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (288) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [0b/0857e3] process > BaseRecalibrator (F_Aln-SNP... [ 25%] 175 of 702 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (288) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [cd/d52092] process > BaseRecalibrator (F_Aln-SNP... [ 24%] 176 of 726 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (288) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [cd/d52092] process > BaseRecalibrator (F_Aln-SNP... [ 24%] 176 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (289) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [13/294e5a] process > BaseRecalibrator (F_Aln-SNP... [ 24%] 176 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (289) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [9f/327787] process > BaseRecalibrator (F_Aln-SNP... [ 24%] 177 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (293) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [14/d56884] process > BaseRecalibrator (F_Aln-SNP... [ 25%] 187 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (296) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [fe/00b31c] process > BaseRecalibrator (F_Aln-SNP... [ 25%] 187 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (299) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [84/a26ee2] process > BaseRecalibrator (F_Aln-SNP... [ 25%] 187 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (300) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [4f/45a786] process > BaseRecalibrator (F_Aln-SNP... [ 25%] 187 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (300) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [b7/efab23] process > BaseRecalibrator (F_Aln-SNP... [ 26%] 194 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (302) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [ab/82398c] process > BaseRecalibrator (F_Aln-SNP... [ 27%] 197 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (305) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [99/536080] process > BaseRecalibrator (F_Aln-SNP... [ 27%] 197 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (308) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [ef/57549f] process > BaseRecalibrator (F_Aln-SNP... [ 27%] 197 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (310) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [51/9654b0] process > BaseRecalibrator (F_Aln-SNP... [ 27%] 197 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (311) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [55/b69346] process > BaseRecalibrator (F_Aln-SNP... [ 28%] 207 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (315) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [72/2a1206] process > BaseRecalibrator (F_Aln-SNP... [ 29%] 211 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (320) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [5f/2e4741] process > BaseRecalibrator (F_Aln-SNP... [ 29%] 211 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (323) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [76/a8522a] process > BaseRecalibrator (F_Aln-SNP... [ 29%] 211 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (324) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [5e/6ad5fc] process > BaseRecalibrator (F_Aln-SNP... [ 29%] 211 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (325) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [5e/03929f] process > BaseRecalibrator (F_Aln-SNP... [ 30%] 223 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (328) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [ae/e41d83] process > BaseRecalibrator (F_Aln-SNP... [ 30%] 224 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (331) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [a8/00dfa9] process > BaseRecalibrator (F_Aln-SNP... [ 30%] 224 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (334) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [db/a80dde] process > BaseRecalibrator (F_Aln-SNP... [ 30%] 224 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (337) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [85/c7417b] process > BaseRecalibrator (F_Aln-SNP... [ 30%] 224 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (337) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [26/75e60a] process > BaseRecalibrator (F_Aln-SNP... [ 30%] 225 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (338) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [e7/921d83] process > BaseRecalibrator (F_Aln-SNP... [ 30%] 225 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (338) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [44/b4c9b2] process > BaseRecalibrator (F_Aln-SNP... [ 31%] 228 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (341) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [aa/360eed] process > BaseRecalibrator (F_Aln-SNP... [ 31%] 233 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (344) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [b5/bfddc7] process > BaseRecalibrator (F_Aln-SNP... [ 31%] 233 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (346) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [0d/03ece6] process > BaseRecalibrator (F_Aln-SNP... [ 31%] 233 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (346) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [e1/e25af9] process > BaseRecalibrator (F_Aln-SNP... [ 32%] 238 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (348) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [f4/121d29] process > BaseRecalibrator (F_Aln-SNP... [ 34%] 250 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (351) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [56/437e79] process > BaseRecalibrator (F_Aln-SNP... [ 34%] 250 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (355) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [fb/618e26] process > BaseRecalibrator (F_Aln-SNP... [ 34%] 250 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (359) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [59/18b110] process > BaseRecalibrator (F_Aln-SNP... [ 34%] 250 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (362) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [7c/a41bbc] process > BaseRecalibrator (F_Aln-SNP... [ 34%] 250 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (363) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [84/7a3fdc] process > BaseRecalibrator (F_Aln-SNP... [ 34%] 250 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (363) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [5f/399ea2] process > BaseRecalibrator (F_Aln-SNP... [ 34%] 253 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (366) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [44/4f0b37] process > BaseRecalibrator (F_Aln-SNP... [ 36%] 265 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (368) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [da/486f5d] process > BaseRecalibrator (F_Aln-SNP... [ 36%] 265 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (371) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [79/6b0272] process > BaseRecalibrator (F_Aln-SNP... [ 36%] 265 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (375) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2e/0759c5] process > BaseRecalibrator (F_Aln-SNP... [ 36%] 265 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (378) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [f1/32e0ba] process > BaseRecalibrator (F_Aln-SNP... [ 36%] 265 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (379) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [39/013b22] process > BaseRecalibrator (F_Aln-SNP... [ 37%] 276 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (381) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [e0/12d712] process > BaseRecalibrator (F_Aln-SNP... [ 39%] 292 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (384) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [ 39%] 292 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (386) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [b9/f7a853] process > BaseRecalibrator (F_Aln-SNP... [ 39%] 292 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (389) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [c2/41ebe7] process > BaseRecalibrator (F_Aln-SNP... [ 39%] 292 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (393) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [ca/2de9e0] process > BaseRecalibrator (F_Aln-SNP... [ 39%] 292 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (398) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [c9/18bfc0] process > BaseRecalibrator (F_Aln-SNP... [ 39%] 292 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (400) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [fe/2d337b] process > BaseRecalibrator (F_Aln-SNP... [ 39%] 292 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (404) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [b7/7f4dbb] process > BaseRecalibrator (F_Aln-SNP... [ 39%] 292 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (405) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [a4/1cc14b] process > BaseRecalibrator (F_Aln-SNP... [ 39%] 292 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (405) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [5f/2e4741] process > BaseRecalibrator (F_Aln-SNP... [ 40%] 293 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (407) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [36/53aeda] process > BaseRecalibrator (F_Aln-SNP... [ 40%] 294 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (408) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [1e/fcec90] process > BaseRecalibrator (F_Aln-SNP... [ 40%] 296 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (412) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [15/2dd557] process > BaseRecalibrator (F_Aln-SNP... [ 41%] 300 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (413) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [df/1275f4] process > BaseRecalibrator (F_Aln-SNP... [ 41%] 300 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (415) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [7c/a41bbc] process > BaseRecalibrator (F_Aln-SNP... [ 42%] 310 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (419) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [90/8b80e1] process > BaseRecalibrator (F_Aln-SNP... [ 42%] 313 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (423) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [d4/50ee1e] process > BaseRecalibrator (F_Aln-SNP... [ 42%] 313 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (426) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [01/5e41df] process > BaseRecalibrator (F_Aln-SNP... [ 42%] 313 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (426) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [7c/ed8bfd] process > BaseRecalibrator (F_Aln-SNP... [ 43%] 316 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (429) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [71/cc9a1a] process > BaseRecalibrator (F_Aln-SNP... [ 44%] 323 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (433) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [ee/87c2a8] process > BaseRecalibrator (F_Aln-SNP... [ 44%] 323 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (436) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [28/336646] process > BaseRecalibrator (F_Aln-SNP... [ 44%] 323 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (438) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [59/18b110] process > BaseRecalibrator (F_Aln-SNP... [ 45%] 336 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (442) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [ac/e60136] process > BaseRecalibrator (F_Aln-SNP... [ 47%] 346 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (446) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [fc/c0ab81] process > BaseRecalibrator (F_Aln-SNP... [ 47%] 346 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (450) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [b5/d012ec] process > BaseRecalibrator (F_Aln-SNP... [ 47%] 346 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (457) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [d5/2f8959] process > BaseRecalibrator (F_Aln-SNP... [ 47%] 346 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (459) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [dd/af5aac] process > BaseRecalibrator (F_Aln-SNP... [ 47%] 346 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (462) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [66/e7e8c3] process > BaseRecalibrator (F_Aln-SNP... [ 47%] 349 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (466) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [25/0c1739] process > BaseRecalibrator (F_Aln-SNP... [ 49%] 360 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (471) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [cd/8ee97a] process > BaseRecalibrator (F_Aln-SNP... [ 49%] 360 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (473) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [15/187105] process > BaseRecalibrator (F_Aln-SNP... [ 49%] 360 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (473) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [a4/1cc14b] process > BaseRecalibrator (F_Aln-SNP... [ 49%] 362 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (479) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [c1/331bf9] process > BaseRecalibrator (F_Aln-SNP... [ 49%] 366 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (479) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [91/13e34c] process > BaseRecalibrator (F_Aln-SNP... [ 50%] 371 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (482) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [08/b28939] process > BaseRecalibrator (F_Aln-SNP... [ 51%] 381 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (485) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [60/3a37dc] process > BaseRecalibrator (F_Aln-SNP... [ 51%] 381 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (490) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [56/6c3049] process > BaseRecalibrator (F_Aln-SNP... [ 51%] 381 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (494) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [61/2c2c62] process > BaseRecalibrator (F_Aln-SNP... [ 51%] 381 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (496) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [9b/d36cf9] process > BaseRecalibrator (F_Aln-SNP... [ 52%] 387 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (500) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [ba/43344c] process > BaseRecalibrator (F_Aln-SNP... [ 52%] 387 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (501) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [d5/20ab21] process > BaseRecalibrator (F_Aln-SNP... [ 52%] 388 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (502) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [06/09515c] process > BaseRecalibrator (F_Aln-SNP... [ 54%] 398 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (508) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [66/d0aa4f] process > BaseRecalibrator (F_Aln-SNP... [ 54%] 400 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (511) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/061567] process > BaseRecalibrator (F_Aln-SNP... [ 54%] 400 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (513) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [57/d7e6f1] process > BaseRecalibrator (F_Aln-SNP... [ 54%] 400 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (517) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [b1/55e8b8] process > BaseRecalibrator (F_Aln-SNP... [ 55%] 405 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (518) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [60/81bff6] process > BaseRecalibrator (F_Aln-SNP... [ 55%] 405 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (521) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [81/d03579] process > BaseRecalibrator (F_Aln-SNP... [ 58%] 429 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (525) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [84/ee5b5c] process > BaseRecalibrator (F_Aln-SNP... [ 58%] 429 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (531) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [58/f92f1b] process > BaseRecalibrator (F_Aln-SNP... [ 58%] 429 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (536) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [37/85d3f7] process > BaseRecalibrator (F_Aln-SNP... [ 58%] 429 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (542) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [aa/095974] process > BaseRecalibrator (F_Aln-SNP... [ 58%] 429 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (542) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [77/1ea312] process > BaseRecalibrator (F_Aln-SNP... [ 58%] 432 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (547) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [25/494fec] process > BaseRecalibrator (F_Aln-SNP... [ 59%] 434 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (547) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [82/d06981] process > BaseRecalibrator (F_Aln-SNP... [ 59%] 435 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (548) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [22/d7834d] process > BaseRecalibrator (F_Aln-SNP... [ 59%] 435 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (548) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [d7/c84eb1] process > BaseRecalibrator (F_Aln-SNP... [ 59%] 436 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (551) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [7c/384a1b] process > BaseRecalibrator (F_Aln-SNP... [ 59%] 438 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (552) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [e7/0aae37] process > BaseRecalibrator (F_Aln-SNP... [ 60%] 444 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (557) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [24/397ae7] process > BaseRecalibrator (F_Aln-SNP... [ 60%] 445 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (558) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [6c/21cc4b] process > BaseRecalibrator (F_Aln-SNP... [ 60%] 445 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (559) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [b1/55e8b8] process > BaseRecalibrator (F_Aln-SNP... [ 61%] 451 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (564) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [e0/17bec3] process > BaseRecalibrator (F_Aln-SNP... [ 61%] 451 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (565) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [7f/d251d2] process > BaseRecalibrator (F_Aln-SNP... [ 62%] 462 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (571) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [45/e1b6e6] process > BaseRecalibrator (F_Aln-SNP... [ 64%] 474 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (574) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [d6/43ac84] process > BaseRecalibrator (F_Aln-SNP... [ 64%] 474 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (580) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [98/b57e8e] process > BaseRecalibrator (F_Aln-SNP... [ 64%] 474 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (585) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [f2/84478d] process > BaseRecalibrator (F_Aln-SNP... [ 64%] 474 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (587) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [15/0578a3] process > BaseRecalibrator (F_Aln-SNP... [ 64%] 474 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (591) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [4c/b6fa05] process > BaseRecalibrator (F_Aln-SNP... [ 65%] 478 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (592) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [95/6ee8e6] process > BaseRecalibrator (F_Aln-SNP... [ 65%] 479 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (595) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [e0/17bec3] process > BaseRecalibrator (F_Aln-SNP... [ 66%] 492 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (601) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [87/d71fe1] process > BaseRecalibrator (F_Aln-SNP... [ 66%] 492 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (605) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [d2/b0239d] process > BaseRecalibrator (F_Aln-SNP... [ 66%] 492 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (610) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [7c/f2ad7f] process > BaseRecalibrator (F_Aln-SNP... [ 67%] 497 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (610) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [9b/d36cf9] process > BaseRecalibrator (F_Aln-SNP... [ 67%] 498 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (613) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [58/37fdb1] process > BaseRecalibrator (F_Aln-SNP... [ 71%] 522 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (618) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [84/566e11] process > BaseRecalibrator (F_Aln-SNP... [ 71%] 522 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (623) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [48/94d92f] process > BaseRecalibrator (F_Aln-SNP... [ 71%] 522 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (629) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [71/60f525] process > BaseRecalibrator (F_Aln-SNP... [ 71%] 522 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (635) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [9f/1c8f96] process > BaseRecalibrator (F_Aln-SNP... [ 71%] 522 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (637) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [8a/b8a23b] process > BaseRecalibrator (F_Aln-SNP... [ 71%] 524 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (638) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [cf/1dcc1e] process > BaseRecalibrator (F_Aln-SNP... [ 71%] 525 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (641) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [b8/ddcb80] process > BaseRecalibrator (F_Aln-SNP... [ 72%] 535 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (647) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [f7/7ba466] process > BaseRecalibrator (F_Aln-SNP... [ 73%] 537 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (650) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [73/700c7d] process > BaseRecalibrator (F_Aln-SNP... [ 73%] 537 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (653) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [9a/c9b2a5] process > BaseRecalibrator (F_Aln-SNP... [ 73%] 542 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (655) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [63/c0923d] process > BaseRecalibrator (F_Aln-SNP... [ 73%] 542 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (658) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [72/92adbd] process > BaseRecalibrator (F_Aln-SNP... [ 76%] 565 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (662) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [cf/bbb825] process > BaseRecalibrator (F_Aln-SNP... [ 77%] 572 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (667) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [61/7bc99e] process > BaseRecalibrator (F_Aln-SNP... [ 77%] 572 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (673) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [11/a6fe03] process > BaseRecalibrator (F_Aln-SNP... [ 77%] 572 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (679) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [c1/1e354a] process > BaseRecalibrator (F_Aln-SNP... [ 77%] 572 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (685) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/9ed123] process > BaseRecalibrator (F_Aln-SNP... [ 77%] 572 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (688) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [50/70c609] process > BaseRecalibrator (F_Aln-SNP... [ 78%] 576 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (689) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [63/764d5f] process > BaseRecalibrator (F_Aln-SNP... [ 78%] 576 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (689) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [aa/c9a029] process > BaseRecalibrator (F_Aln-SNP... [ 78%] 577 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (690) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [a9/7389c2] process > BaseRecalibrator (F_Aln-SNP... [ 78%] 577 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (690) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [cb/758783] process > BaseRecalibrator (F_Aln-SNP... [ 79%] 581 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (694) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [30/9b7453] process > BaseRecalibrator (F_Aln-SNP... [ 80%] 590 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (700) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [d8/b7fd0c] process > BaseRecalibrator (F_Aln-SNP... [ 80%] 590 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (703) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [a4/d2ff69] process > BaseRecalibrator (F_Aln-SNP... [ 80%] 590 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (704) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [9b/06ec76] process > BaseRecalibrator (F_Aln-SNP... [ 80%] 592 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (705) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [d5/e23ee9] process > BaseRecalibrator (F_Aln-SNP... [ 80%] 592 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (705) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [9f/1c8f96] process > BaseRecalibrator (F_Aln-SNP... [ 81%] 600 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (708) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [f1/319e21] process > BaseRecalibrator (F_Aln-SNP... [ 83%] 613 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (714) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [8e/c31130] process > BaseRecalibrator (F_Aln-SNP... [ 83%] 613 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (719) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [6e/a58a0c] process > BaseRecalibrator (F_Aln-SNP... [ 83%] 613 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (725) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [52/8d2db9] process > BaseRecalibrator (F_Aln-SNP... [ 83%] 613 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (726) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [19/24edc3] process > BaseRecalibrator (F_Aln-SNP... [ 83%] 613 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (727) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [40/d50ed2] process > BaseRecalibrator (F_Aln-SNP... [ 83%] 617 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (730) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [9c/ecf91a] process > BaseRecalibrator (F_Aln-SNP... [ 83%] 617 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (731) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [4c/bf8b3e] process > BaseRecalibrator (F_Aln-SNP... [ 84%] 618 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (732) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [79/e14b06] process > BaseRecalibrator (F_Aln-SNP... [ 84%] 619 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (734) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [1d/66fe2b] process > BaseRecalibrator (F_Aln-SNP... [ 85%] 628 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (740) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [cc/b3288c] process > BaseRecalibrator (F_Aln-SNP... [ 85%] 632 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (745) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [01/de483c] process > BaseRecalibrator (F_Aln-SNP... [ 85%] 632 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (747) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [02/0e8828] process > BaseRecalibrator (F_Aln-SNP... [ 86%] 634 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (751) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [e0/af9183] process > BaseRecalibrator (F_Aln-SNP... [ 89%] 655 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (751) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [3f/29a651] process > BaseRecalibrator (F_Aln-SNP... [ 89%] 656 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [6a/e609b1] process > BaseRecalibrator (F_Aln-SNP... [ 89%] 656 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [51/3416ad] process > BaseRecalibrator (F_Aln-SNP... [ 89%] 658 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [de/d2f0f4] process > BaseRecalibrator (F_Aln-SNP... [ 90%] 665 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [de/d2f0f4] process > BaseRecalibrator (F_Aln-SNP... [ 90%] 665 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [8e/c31130] process > BaseRecalibrator (F_Aln-SNP... [ 90%] 668 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [aa/1a7201] process > BaseRecalibrator (F_Aln-SNP... [ 91%] 676 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [b0/77c07f] process > BaseRecalibrator (F_Aln-SNP... [ 92%] 680 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [25/642217] process > BaseRecalibrator (F_Aln-SNP... [ 92%] 681 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [48/3cd5e5] process > BaseRecalibrator (F_Aln-SNP... [ 93%] 690 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [66/2c4819] process > BaseRecalibrator (F_Aln-SNP... [ 96%] 709 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [1c/5ecf86] process > BaseRecalibrator (F_Aln-SNP... [ 96%] 712 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [34/114443] process > BaseRecalibrator (F_Aln-SNP... [ 96%] 714 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [6a/e609b1] process > BaseRecalibrator (F_Aln-SNP... [ 97%] 718 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [db/e26b14] process > BaseRecalibrator (F_Aln-SNP... [ 97%] 720 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [99/c72312] process > BaseRecalibrator (F_Aln-SNP... [ 97%] 721 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [24/8b4e7b] process > BaseRecalibrator (F_Aln-SNP... [ 98%] 722 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [f8/4a0684] process > BaseRecalibrator (F_Aln-SNP... [ 98%] 723 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [11/a6fe03] process > BaseRecalibrator (F_Aln-SNP... [ 98%] 724 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [23/8f8991] process > BaseRecalibrator (F_Aln-SNP... [ 98%] 725 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [29/89703e] process > BaseRecalibrator (F_Aln-SNP... [ 98%] 726 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [27/f10047] process > BaseRecalibrator (F_Aln-SNP... [ 98%] 727 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [f5/091546] process > BaseRecalibrator (F_Aln-SNP... [ 99%] 729 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [c3/1693cb] process > BaseRecalibrator (F_Aln-SNP... [ 99%] 730 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [77/b00e28] process > BaseRecalibrator (F_Aln-SNP... [ 99%] 731 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [b9/f7a853] process > BaseRecalibrator (F_Aln-SNP... [ 99%] 732 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [a9/4654a8] process > BaseRecalibrator (F_Aln-SNP... [ 99%] 733 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [d0/6324c8] process > BaseRecalibrator (F_Aln-SNP... [ 99%] 734 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/c7d590] process > BaseRecalibrator (F_Aln-SNP... [ 99%] 735 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [37/0745b7] process > BaseRecalibrator (F_Aln-SNP... [ 99%] 736 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [68/87646f] process > BaseRecalibrator (F_Aln-SNP... [100%] 737 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [b2/497484] process > BaseRecalibrator (F_Aln-SNP... [100%] 738 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/b79d11] process > BaseRecalibrator (F_Aln-SNP... [100%] 739 of 740 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [- ] process > GatherBQSRReports [ 0%] 0 of 1 [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (754) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [62/257823] process > GatherBQSRReports (F_Aln-SN... [ 0%] 0 of 2 [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (755) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [ 0%] 0 of 2 [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (755) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [ 0%] 0 of 2 [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (755) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [62/257823] process > GatherBQSRReports (F_Aln-SN... [ 50%] 1 of 2 [- ] process > ApplyBQSR [ 0%] 0 of 6 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (756) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [62/257823] process > GatherBQSRReports (F_Aln-SN... [ 50%] 1 of 2 [3c/25ca58] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 395 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (756) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [3c/25ca58] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 447 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (756) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [3c/25ca58] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 504 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (756) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [3c/25ca58] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 553 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (756) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [3c/25ca58] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 604 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (757) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [0a/73965b] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (760) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [3c/c52e6b] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (764) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [2b/114d2f] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (769) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [cd/0564a3] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (775) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [f4/487874] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (781) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [3b/b6432d] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (787) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [27/305deb] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (792) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [84/61c4a4] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (798) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [c9/9b356c] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (804) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [c8/f3f9d2] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (810) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [b2/e8405f] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (816) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [6a/e13a4a] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (823) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [03/52f88b] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (829) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [ee/1818b6] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (835) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [2e/396859] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (842) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [cb/3aa39a] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (847) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [9d/a8d35e] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (853) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [8c/03960d] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (855) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a3/a83ffd] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (855) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a3/a83ffd] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (855) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a3/a83ffd] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (855) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a3/a83ffd] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (855) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a3/a83ffd] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (856) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [d1/a87f22] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 1 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (857) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [61/e8221f] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 2%] 12 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (858) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [d3/2889b9] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 5%] 35 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (859) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [1d/b4f6bf] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 7%] 53 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (861) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [07/8b457c] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 9%] 66 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (865) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a6/d22789] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 9%] 66 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (868) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [ae/762d18] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 9%] 66 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (873) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [5e/982aa6] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 9%] 66 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (879) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [3d/10a9d6] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 9%] 66 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (885) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [b3/c6234f] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 9%] 66 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (890) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [1a/43e879] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 9%] 66 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (895) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [cd/e1b332] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 9%] 66 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (901) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [f5/e780da] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 9%] 66 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (906) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [48/96ee10] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 9%] 66 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (912) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [71/a8f369] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 9%] 66 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (917) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [45/7345af] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 9%] 66 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (920) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [47/6a5b9a] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 9%] 66 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (921) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [96/5c068f] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 9%] 66 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (923) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [ba/fde4dd] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 10%] 76 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (929) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [0d/41b148] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 10%] 76 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (931) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [72/4c6272] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 10%] 76 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (932) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [e9/1ebc82] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 10%] 77 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (933) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [41/c8fd15] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 11%] 78 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (933) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [41/c8fd15] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 11%] 78 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (933) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [41/c8fd15] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 11%] 78 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (937) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [4a/9bfbee] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 11%] 82 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (940) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [00/43de33] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 12%] 86 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (941) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a2/8814be] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 12%] 86 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (942) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [3d/10a9d6] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 15%] 108 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (945) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [5c/a5c3ae] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 18%] 136 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (948) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [45/ded3c1] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 20%] 149 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (952) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [49/8ff339] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 20%] 149 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (957) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [e5/2fe94e] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 20%] 149 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (961) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [db/5c02ad] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 20%] 149 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (968) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [4b/19b7dc] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 20%] 149 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (974) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [d8/422199] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 20%] 149 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (980) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [0e/b9bed0] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 20%] 149 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (986) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [c6/b944b1] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 20%] 149 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (992) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [af/7090f7] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 20%] 149 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (998) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [40/d45c13] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 20%] 149 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1004) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [69/f4c569] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 20%] 149 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1005) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [ca/b12399] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 21%] 155 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1010) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [e3/5496ac] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 21%] 155 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1011) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a3/436965] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 21%] 156 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1011) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a3/436965] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 21%] 156 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1011) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a3/436965] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 21%] 156 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1011) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a3/436965] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 21%] 156 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1012) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [63/3541e5] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 21%] 157 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1014) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [aa/842662] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 22%] 160 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1015) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [99/716ab4] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 22%] 160 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1016) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [79/5e997f] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 23%] 173 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1020) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [28/b69dd7] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 27%] 201 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1021) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [f8/ef619b] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 30%] 222 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1023) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [2a/ea9af9] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 31%] 231 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1025) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [6c/669f45] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 31%] 231 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1030) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [cb/4e51f4] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 31%] 231 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1035) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [0a/110589] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 31%] 231 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1040) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [34/89430d] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 31%] 231 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1045) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [17/cf096e] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 31%] 231 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1051) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [98/b35bf3] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 31%] 231 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1057) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [38/290cef] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 31%] 231 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1063) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [72/a45958] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 31%] 231 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1070) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [17/2e08ad] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 31%] 231 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1077) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [f5/3d96c9] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 31%] 231 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1083) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [53/225008] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 31%] 231 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1086) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [1c/25912a] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 31%] 231 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1088) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [0d/08fcb1] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 32%] 238 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1093) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [50/855e6c] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 32%] 238 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1095) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [5d/8610c6] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 32%] 240 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1095) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [5d/8610c6] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 32%] 240 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1095) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [5d/8610c6] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 32%] 240 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1095) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [63/3541e5] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 33%] 241 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1099) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [59/a96342] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 33%] 244 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1099) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [66/03c297] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 34%] 248 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1101) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a7/95c1ef] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 36%] 270 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1103) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [17/2e08ad] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 40%] 296 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1105) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [91/d50206] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 42%] 313 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1111) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [54/ecbc4b] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 42%] 313 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1116) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [16/eb47f8] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 42%] 313 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1121) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [2b/484704] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 42%] 313 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1127) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [29/f1e1d6] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 42%] 313 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1131) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [4f/c4246e] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 42%] 313 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1136) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [66/7fbf16] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 42%] 313 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1142) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a2/996396] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 42%] 313 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1148) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [51/3949b8] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 42%] 313 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1154) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [0c/f71616] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 42%] 313 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1160) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [17/eb3c45] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 42%] 313 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1166) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 42%] 313 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1168) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [dd/aa3609] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 42%] 313 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1170) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [8e/269cf8] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 44%] 322 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1176) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [c8/e26330] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 44%] 322 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1177) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [c4/d1f5a6] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 44%] 322 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1178) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [43/4b4475] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 44%] 323 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1178) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [43/4b4475] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 44%] 323 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1178) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [43/4b4475] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 44%] 323 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1178) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [43/4b4475] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 44%] 323 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1179) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [4f/3c2e8d] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 44%] 328 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1182) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [6d/edf289] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 44%] 328 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1183) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [fd/1d4ea5] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 44%] 328 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1187) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [83/c134e6] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 47%] 350 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1188) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [16/648314] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 49%] 360 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1191) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [bf/97a5cc] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 50%] 373 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1196) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [2a/9963bf] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 50%] 373 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1202) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [92/d0c42e] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 50%] 373 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1206) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [c6/ab40bd] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 50%] 373 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1209) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [81/f79d55] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 50%] 373 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1215) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [2b/e69994] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 50%] 373 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1218) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [f3/f0f72e] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 50%] 373 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1223) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [76/d2b1d6] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 50%] 373 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1228) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [8e/f450ad] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 50%] 373 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1231) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [bb/2ebd1e] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 53%] 390 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1237) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [21/215429] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 53%] 390 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1243) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [1d/89162d] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 53%] 390 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1245) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [18/e8fc9b] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 53%] 390 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1247) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [dd/21e514] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 53%] 392 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1247) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [dd/21e514] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 53%] 392 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1247) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [dd/21e514] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 53%] 392 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1247) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [dd/21e514] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 53%] 392 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1247) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [01/bf2aa4] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 53%] 393 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1250) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [19/44c0c8] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 53%] 395 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1250) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [25/ab26d2] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 54%] 398 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1252) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [03/6cd139] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 59%] 433 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1256) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [1a/239702] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 60%] 445 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1260) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [05/71fcaa] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 60%] 445 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1263) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [2f/c4b754] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 60%] 445 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1265) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [d2/777097] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 60%] 445 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1270) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7f/f5e691] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 60%] 445 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1274) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [d2/6004d3] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 60%] 445 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1280) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a7/c1b830] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 60%] 445 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1285) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [36/51fc5f] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 60%] 445 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1291) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [be/2d7218] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 60%] 445 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1297) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [c2/da1510] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 60%] 445 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1300) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [3b/5150aa] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 60%] 445 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1303) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [62/12dd8b] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 62%] 456 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1310) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [c3/594141] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 62%] 456 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1311) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [b0/54cf74] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 62%] 456 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1312) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [c6/84520a] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 62%] 457 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1313) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [0f/b3f9c3] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 62%] 458 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1313) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [0f/b3f9c3] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 62%] 458 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1315) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [72/82c7e1] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 62%] 460 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1317) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [e0/e34b55] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 62%] 462 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1317) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [dd/fc96b5] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 63%] 463 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1320) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [30/cf3929] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 66%] 490 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1320) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [c2/da1510] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 68%] 506 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1321) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [c3/594141] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 70%] 517 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1323) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [61/cc8baa] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 70%] 520 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1325) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [6f/b9e046] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 70%] 520 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1328) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [0c/26c3bc] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 70%] 520 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1332) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [89/74f107] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 70%] 520 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1337) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [5e/819668] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 70%] 520 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1343) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [72/6db25c] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 70%] 520 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1349) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [e7/84bc81] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 70%] 520 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1355) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [dd/417e8f] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 70%] 520 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1361) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [41/54cc7d] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 70%] 520 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1368) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [8d/040ad1] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 70%] 520 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1372) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [2f/c967ad] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 70%] 520 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1375) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [1e/97fb9a] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 70%] 520 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1375) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [3b/5150aa] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 71%] 526 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1381) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [3a/1b3c8c] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 71%] 526 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1382) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [f4/791c62] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 71%] 527 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1382) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [f4/791c62] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 71%] 527 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1382) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [f4/791c62] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 71%] 527 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1382) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [f4/791c62] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 71%] 527 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1383) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [aa/343e3d] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 71%] 528 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1386) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [92/7a15d1] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 72%] 531 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1388) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [e7/ab3c79] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 74%] 549 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1390) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [9f/2435d7] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 78%] 576 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1393) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [5a/abe841] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 79%] 586 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1399) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [24/baea1f] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 79%] 586 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1403) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [63/ae9e70] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 79%] 586 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1409) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [38/b0027f] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 79%] 586 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1414) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [47/0dcf18] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 79%] 586 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1419) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [8f/668f8b] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 79%] 586 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1425) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [fd/875b44] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 79%] 586 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1430) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [f4/5fb899] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 79%] 586 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1433) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [cf/304dee] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 79%] 586 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1439) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [5e/c4daa4] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 79%] 586 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1441) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [1a/0f8467] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 79%] 586 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1446) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [57/7dacc7] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 81%] 599 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1452) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [04/71fdf7] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 81%] 599 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1454) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [3e/c4bcb2] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 81%] 599 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1454) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [aa/5948d6] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 81%] 600 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1455) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [b9/f6200f] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 81%] 600 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1455) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [6f/721dc6] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 81%] 602 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1457) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [2a/a3621a] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 81%] 602 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1457) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [2a/a3621a] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 81%] 602 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1459) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [f0/c00b5f] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 82%] 605 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1460) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [8a/6b04a7] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 82%] 605 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1462) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [f0/8c1097] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 84%] 619 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1464) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7a/bd59ec] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 87%] 645 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1467) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [42/4622fc] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 89%] 656 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1468) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [78/01fc07] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 89%] 656 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1471) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [ca/009168] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 89%] 656 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1474) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [66/8564e9] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 89%] 656 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1478) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [11/36e304] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 89%] 656 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1481) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [3b/482fa9] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 89%] 656 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1484) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [c8/82d4da] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 89%] 656 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1488) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [ad/6e7beb] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 89%] 656 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1492) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [9d/aa27eb] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 89%] 656 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [f1/de999d] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 89%] 656 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [ff/6eb4d6] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 91%] 673 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [ad/cbee9e] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 91%] 677 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [aa/343e3d] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 92%] 680 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [0f/c95475] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 92%] 681 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [0f/c95475] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 92%] 681 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [ed/706ef4] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 93%] 685 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [96/17e2fe] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 93%] 687 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [63/09e200] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 96%] 714 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [f1/de999d] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 97%] 718 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [f1/3d3f04] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 98%] 722 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [1d/5de9ae] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 98%] 723 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [bd/85b241] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 98%] 725 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [86/53cedd] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 98%] 726 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [43/4b4475] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 98%] 727 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [8f/714ee5] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 98%] 728 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [0a/73965b] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 99%] 729 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [63/555f98] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 99%] 730 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [48/875052] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 99%] 731 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [28/c87418] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 99%] 732 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [6d/edf289] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 99%] 734 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [f4/82b498] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 99%] 735 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [74/f97878] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 99%] 736 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [83/c134e6] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 737 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [09/984faa] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 738 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [3d/fe0e46] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 739 of 740 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal [ 0%] 0 of 1 [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1497) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [ 0%] 0 of 2 [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1497) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [ 0%] 0 of 2 [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1497) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [ 0%] 0 of 2 [- ] process > IndexBamRecal - [- ] process > SamtoolsStats [ 0%] 0 of 1 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle [ 0%] 0 of 12 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1498) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [d3/4f9e40] process > MergeBamRecal (F_Aln-SNP-SR... [ 50%] 1 of 2 [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 1 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller [ 0%] 0 of 341 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle [ 0%] 0 of 99 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1498) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [d3/4f9e40] process > MergeBamRecal (F_Aln-SNP-SR... [ 50%] 1 of 2 [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 1 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [100%] 2 of 2 [- ] process > HaplotypeCaller [ 0%] 0 of 341 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle [ 0%] 0 of 137 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1498) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [d3/4f9e40] process > MergeBamRecal (F_Aln-SNP-SR... [ 50%] 1 of 2 [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 1 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 67%] 2 of 3 [- ] process > HaplotypeCaller [ 0%] 0 of 341 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle [ 0%] 0 of 146 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 1 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1499) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [d3/4f9e40] process > MergeBamRecal (F_Aln-SNP-SR... [ 50%] 1 of 2 [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 1 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 67%] 2 of 3 [- ] process > HaplotypeCaller [ 0%] 0 of 341 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e0/5443f2] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 148 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 11 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1500) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [d3/4f9e40] process > MergeBamRecal (F_Aln-SNP-SR... [ 50%] 1 of 2 [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 1 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 67%] 2 of 3 [- ] process > HaplotypeCaller [ 0%] 0 of 341 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/0408c4] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 148 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 24 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1501) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [d3/4f9e40] process > MergeBamRecal (F_Aln-SNP-SR... [ 50%] 1 of 2 [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 1 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 67%] 2 of 3 [- ] process > HaplotypeCaller [ 0%] 0 of 341 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/0408c4] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 148 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 194 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1501) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [d3/4f9e40] process > MergeBamRecal (F_Aln-SNP-SR... [ 50%] 1 of 2 [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 1 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 67%] 2 of 3 [- ] process > HaplotypeCaller [ 0%] 0 of 370 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9b/f58ca0] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 370 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 370 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1502) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [d3/4f9e40] process > MergeBamRecal (F_Aln-SNP-SR... [ 50%] 1 of 2 [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 1 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 67%] 2 of 3 [- ] process > HaplotypeCaller [ 0%] 0 of 370 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [fe/c3951c] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 370 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 370 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1504) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [d3/4f9e40] process > MergeBamRecal (F_Aln-SNP-SR... [ 50%] 1 of 2 [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 1 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 67%] 2 of 3 [- ] process > HaplotypeCaller [ 0%] 0 of 370 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [dc/60da3f] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 370 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 370 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1507) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [d3/4f9e40] process > MergeBamRecal (F_Aln-SNP-SR... [ 50%] 1 of 2 [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 1 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 67%] 2 of 3 [- ] process > HaplotypeCaller [ 0%] 0 of 370 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [64/734ec7] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 370 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 370 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1509) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [d3/4f9e40] process > MergeBamRecal (F_Aln-SNP-SR... [ 50%] 1 of 2 [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 1 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 67%] 2 of 3 [- ] process > HaplotypeCaller [ 0%] 0 of 370 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [20/dabbe2] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 370 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 370 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1513) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [d3/4f9e40] process > MergeBamRecal (F_Aln-SNP-SR... [ 50%] 1 of 2 [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 1 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 67%] 2 of 3 [- ] process > HaplotypeCaller [ 0%] 0 of 370 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [79/d14835] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 370 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 370 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1517) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [d3/4f9e40] process > MergeBamRecal (F_Aln-SNP-SR... [ 50%] 1 of 2 [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 1 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 67%] 2 of 3 [- ] process > HaplotypeCaller [ 0%] 0 of 370 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9c/d6b801] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 370 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 370 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1521) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [d3/4f9e40] process > MergeBamRecal (F_Aln-SNP-SR... [ 50%] 1 of 2 [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 1 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 67%] 2 of 3 [- ] process > HaplotypeCaller [ 0%] 0 of 370 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [56/daa830] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 370 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 370 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1525) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [d3/4f9e40] process > MergeBamRecal (F_Aln-SNP-SR... [ 50%] 1 of 2 [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 1 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 67%] 2 of 3 [- ] process > HaplotypeCaller [ 0%] 0 of 370 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a1/bb592b] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 370 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 370 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1526) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [d3/4f9e40] process > MergeBamRecal (F_Aln-SNP-SR... [ 50%] 1 of 2 [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 67%] 2 of 3 [- ] process > HaplotypeCaller [ 0%] 0 of 370 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ba/51c683] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 386 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 373 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1526) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [d3/4f9e40] process > MergeBamRecal (F_Aln-SNP-SR... [ 50%] 1 of 2 [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 67%] 2 of 3 [- ] process > HaplotypeCaller [ 0%] 0 of 370 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ba/51c683] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 396 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 382 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1526) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [d3/4f9e40] process > MergeBamRecal (F_Aln-SNP-SR... [ 50%] 1 of 2 [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [- ] process > HaplotypeCaller [ 0%] 0 of 385 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ba/51c683] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 434 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 390 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1526) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [d3/4f9e40] process > MergeBamRecal (F_Aln-SNP-SR... [ 50%] 1 of 2 [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [- ] process > HaplotypeCaller [ 0%] 0 of 432 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ba/51c683] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 441 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 390 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1527) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [- ] process > HaplotypeCaller [ 0%] 0 of 691 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [69/8936cd] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 734 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1527) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [- ] process > HaplotypeCaller [ 0%] 0 of 716 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [69/8936cd] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 739 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1528) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [- ] process > HaplotypeCaller [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [04/a9c6f2] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1530) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [- ] process > HaplotypeCaller [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [12/e9f834] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1532) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [- ] process > HaplotypeCaller [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [d3/c29590] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1536) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [- ] process > HaplotypeCaller [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0c/3a481a] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1539) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [- ] process > HaplotypeCaller [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f8/d09a1f] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1543) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [- ] process > HaplotypeCaller [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [47/ba6af7] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1546) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [- ] process > HaplotypeCaller [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a1/2d4ca1] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1548) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [- ] process > HaplotypeCaller [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7a/4855ef] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1552) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [- ] process > HaplotypeCaller [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5d/0411ee] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1555) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [- ] process > HaplotypeCaller [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [84/b7bdc8] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1559) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [- ] process > HaplotypeCaller [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [01/0e64cf] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1562) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [- ] process > HaplotypeCaller [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6e/345ac4] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1565) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [- ] process > HaplotypeCaller [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f6/966cd3] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1569) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [12/8cda67] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f6/966cd3] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1572) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [7b/4ab7ba] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f6/966cd3] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1574) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [39/e66f92] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f6/966cd3] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1577) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [a6/46d0a3] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f6/966cd3] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1580) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f6/966cd3] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1583) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [e1/79bb54] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f6/966cd3] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1586) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [a2/defef8] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f6/966cd3] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1590) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [11/7ec508] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f6/966cd3] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1593) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [be/f8b457] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f6/966cd3] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1596) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [c8/a8de3d] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f6/966cd3] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1597) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [7a/b7400e] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f6/966cd3] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1597) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [7a/b7400e] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f6/966cd3] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1597) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [7a/b7400e] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f6/966cd3] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1597) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [7a/b7400e] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f6/966cd3] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1597) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [7a/b7400e] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f6/966cd3] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1597) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [7a/b7400e] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f6/966cd3] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1598) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [d8/d5032d] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [51/444a01] process > FreebayesSingle (SRR7062654... [ 2%] 16 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1600) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [c2/5aa25a] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f6/966cd3] process > FreebayesSingle (SRR7062654... [ 4%] 26 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1603) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [0c/89ed34] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f6/966cd3] process > FreebayesSingle (SRR7062654... [ 4%] 26 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1606) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [4b/8b803e] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f6/966cd3] process > FreebayesSingle (SRR7062654... [ 4%] 26 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1609) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [4a/142efc] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f6/966cd3] process > FreebayesSingle (SRR7062654... [ 4%] 26 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1612) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [f8/d29c37] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f6/966cd3] process > FreebayesSingle (SRR7062654... [ 4%] 26 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1616) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [0c/088318] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f6/966cd3] process > FreebayesSingle (SRR7062654... [ 4%] 26 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1619) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [bc/10f12f] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f6/966cd3] process > FreebayesSingle (SRR7062654... [ 4%] 26 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1622) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [30/8d2c22] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f6/966cd3] process > FreebayesSingle (SRR7062654... [ 4%] 26 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1623) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [d9/6f8720] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f6/966cd3] process > FreebayesSingle (SRR7062654... [ 4%] 26 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1624) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [55/e0ed26] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [c2/546702] process > FreebayesSingle (SRR7062654... [ 5%] 38 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1628) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [7f/81b273] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [21/3d4572] process > FreebayesSingle (SRR7062654... [ 7%] 52 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1631) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [c4/b6c562] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [21/3d4572] process > FreebayesSingle (SRR7062654... [ 7%] 52 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1634) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [69/5abee2] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [21/3d4572] process > FreebayesSingle (SRR7062654... [ 7%] 52 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1637) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [82/306429] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [21/3d4572] process > FreebayesSingle (SRR7062654... [ 7%] 52 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1640) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [08/f57531] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [21/3d4572] process > FreebayesSingle (SRR7062654... [ 7%] 52 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1643) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [d6/f8d613] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [21/3d4572] process > FreebayesSingle (SRR7062654... [ 7%] 52 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1646) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [39/e259b0] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [21/3d4572] process > FreebayesSingle (SRR7062654... [ 7%] 52 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1648) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [73/54c336] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [21/3d4572] process > FreebayesSingle (SRR7062654... [ 7%] 52 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1649) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [47/03b8bb] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [21/3d4572] process > FreebayesSingle (SRR7062654... [ 7%] 52 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1649) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [47/03b8bb] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [30/06d34c] process > FreebayesSingle (SRR7062654... [ 8%] 56 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1653) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [d8/243131] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3d/73d8a8] process > FreebayesSingle (SRR7062654... [ 8%] 57 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1654) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [b7/afc573] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3d/73d8a8] process > FreebayesSingle (SRR7062654... [ 8%] 57 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1654) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [b7/afc573] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [79/d14835] process > FreebayesSingle (SRR7062654... [ 8%] 58 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1655) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [23/f56a1a] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [79/d14835] process > FreebayesSingle (SRR7062654... [ 8%] 58 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1655) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [23/f56a1a] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 740 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [79/d14835] process > FreebayesSingle (SRR7062654... [ 8%] 58 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1656) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [0d/1a4d01] process > HaplotypeCaller (SRR7062654... [ 0%] 1 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 1 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [79/d14835] process > FreebayesSingle (SRR7062654... [ 8%] 58 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1657) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [b9/a13b45] process > HaplotypeCaller (SRR7062654... [ 0%] 2 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 2 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [79/d14835] process > FreebayesSingle (SRR7062654... [ 8%] 58 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1658) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [f4/5bca55] process > HaplotypeCaller (SRR7062654... [ 1%] 4 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 4 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [79/d14835] process > FreebayesSingle (SRR7062654... [ 8%] 58 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1659) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [9b/d5e100] process > HaplotypeCaller (SRR7062654... [ 1%] 4 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 4 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [79/d14835] process > FreebayesSingle (SRR7062654... [ 8%] 58 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1661) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [61/f69814] process > HaplotypeCaller (SRR7062654... [ 1%] 6 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 6 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [79/d14835] process > FreebayesSingle (SRR7062654... [ 8%] 58 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1661) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [d0/088cc0] process > HaplotypeCaller (SRR7062654... [ 1%] 9 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 8 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [79/d14835] process > FreebayesSingle (SRR7062654... [ 8%] 58 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1664) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [d0/1ad95c] process > HaplotypeCaller (SRR7062654... [ 3%] 21 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 21 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [79/d14835] process > FreebayesSingle (SRR7062654... [ 8%] 58 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1667) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [db/6b69f7] process > HaplotypeCaller (SRR7062654... [ 3%] 21 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 21 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [79/d14835] process > FreebayesSingle (SRR7062654... [ 8%] 58 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1670) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [fb/49ad1f] process > HaplotypeCaller (SRR7062654... [ 3%] 21 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 21 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [79/d14835] process > FreebayesSingle (SRR7062654... [ 8%] 58 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1673) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [5a/bd7107] process > HaplotypeCaller (SRR7062654... [ 3%] 21 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 21 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [79/d14835] process > FreebayesSingle (SRR7062654... [ 8%] 58 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1676) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [1e/6cde56] process > HaplotypeCaller (SRR7062654... [ 3%] 21 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 21 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [79/d14835] process > FreebayesSingle (SRR7062654... [ 8%] 58 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1676) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [be/172adc] process > HaplotypeCaller (SRR7062654... [ 3%] 24 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 24 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [79/d14835] process > FreebayesSingle (SRR7062654... [ 8%] 58 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1679) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [ed/0142bd] process > HaplotypeCaller (SRR7062654... [ 4%] 29 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 29 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [79/d14835] process > FreebayesSingle (SRR7062654... [ 8%] 58 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1682) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [67/eec580] process > HaplotypeCaller (SRR7062654... [ 4%] 29 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 29 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [79/d14835] process > FreebayesSingle (SRR7062654... [ 8%] 58 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1684) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [2e/561de0] process > HaplotypeCaller (SRR7062654... [ 4%] 29 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 29 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [79/d14835] process > FreebayesSingle (SRR7062654... [ 8%] 58 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1685) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [c9/79d305] process > HaplotypeCaller (SRR7062654... [ 6%] 41 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 41 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [79/d14835] process > FreebayesSingle (SRR7062654... [ 8%] 58 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1690) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [bf/585d1e] process > HaplotypeCaller (SRR7062654... [ 6%] 41 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 41 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [79/d14835] process > FreebayesSingle (SRR7062654... [ 8%] 58 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1694) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [ca/6dad8f] process > HaplotypeCaller (SRR7062654... [ 6%] 41 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 41 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [79/d14835] process > FreebayesSingle (SRR7062654... [ 8%] 58 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1696) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [12/5961b6] process > HaplotypeCaller (SRR7062654... [ 6%] 41 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 41 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [79/d14835] process > FreebayesSingle (SRR7062654... [ 8%] 58 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1699) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [82/e98083] process > HaplotypeCaller (SRR7062654... [ 6%] 45 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 45 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [79/d14835] process > FreebayesSingle (SRR7062654... [ 8%] 58 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1700) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [60/9aaaf6] process > HaplotypeCaller (SRR7062654... [ 6%] 45 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 45 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [79/d14835] process > FreebayesSingle (SRR7062654... [ 8%] 58 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1703) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [02/6fcc46] process > HaplotypeCaller (SRR7062654... [ 7%] 53 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 53 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e1/6b7266] process > FreebayesSingle (SRR7062654... [ 8%] 59 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1709) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [68/033218] process > HaplotypeCaller (SRR7062654... [ 7%] 53 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 53 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e1/6b7266] process > FreebayesSingle (SRR7062654... [ 8%] 59 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1711) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [4d/8ab06a] process > HaplotypeCaller (SRR7062654... [ 7%] 55 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 55 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e1/6b7266] process > FreebayesSingle (SRR7062654... [ 8%] 59 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1714) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [fe/de7366] process > HaplotypeCaller (SRR7062654... [ 8%] 61 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 61 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e1/6b7266] process > FreebayesSingle (SRR7062654... [ 8%] 59 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1717) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [32/4eeadc] process > HaplotypeCaller (SRR7062654... [ 8%] 61 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 61 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e1/6b7266] process > FreebayesSingle (SRR7062654... [ 8%] 59 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1717) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [61/f69814] process > HaplotypeCaller (SRR7062654... [ 9%] 63 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 63 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [dc/60da3f] process > FreebayesSingle (SRR7062654... [ 8%] 60 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1720) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [0b/fa98b1] process > HaplotypeCaller (SRR7062654... [ 9%] 63 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 63 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [dc/60da3f] process > FreebayesSingle (SRR7062654... [ 8%] 60 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1720) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [55/e0ed26] process > HaplotypeCaller (SRR7062654... [ 9%] 67 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 67 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [dc/60da3f] process > FreebayesSingle (SRR7062654... [ 8%] 60 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1724) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [e4/5f3572] process > HaplotypeCaller (SRR7062654... [ 9%] 67 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 67 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [dc/60da3f] process > FreebayesSingle (SRR7062654... [ 8%] 60 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1724) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [9c/efe403] process > HaplotypeCaller (SRR7062654... [ 9%] 68 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 68 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [dc/60da3f] process > FreebayesSingle (SRR7062654... [ 8%] 60 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1725) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [65/0241a3] process > HaplotypeCaller (SRR7062654... [ 9%] 68 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 68 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [dc/60da3f] process > FreebayesSingle (SRR7062654... [ 8%] 60 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1725) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [b3/ec9238] process > HaplotypeCaller (SRR7062654... [ 10%] 71 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 71 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3e/876243] process > FreebayesSingle (SRR7062654... [ 8%] 61 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1729) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [4a/f884f3] process > HaplotypeCaller (SRR7062654... [ 10%] 71 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 71 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3e/876243] process > FreebayesSingle (SRR7062654... [ 8%] 61 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1730) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [76/79cef2] process > HaplotypeCaller (SRR7062654... [ 10%] 76 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 76 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3e/876243] process > FreebayesSingle (SRR7062654... [ 8%] 61 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1735) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [e2/e062e1] process > HaplotypeCaller (SRR7062654... [ 11%] 79 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 79 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3e/876243] process > FreebayesSingle (SRR7062654... [ 8%] 61 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1737) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [67/186b79] process > HaplotypeCaller (SRR7062654... [ 11%] 79 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 79 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3e/876243] process > FreebayesSingle (SRR7062654... [ 8%] 61 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1738) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [29/5c6f37] process > HaplotypeCaller (SRR7062654... [ 12%] 87 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 87 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3e/876243] process > FreebayesSingle (SRR7062654... [ 8%] 61 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1741) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [76/5cb815] process > HaplotypeCaller (SRR7062654... [ 13%] 95 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 95 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3e/876243] process > FreebayesSingle (SRR7062654... [ 8%] 61 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1746) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [17/451440] process > HaplotypeCaller (SRR7062654... [ 13%] 95 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 95 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3e/876243] process > FreebayesSingle (SRR7062654... [ 8%] 61 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1749) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [ff/67a800] process > HaplotypeCaller (SRR7062654... [ 13%] 95 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 95 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3e/876243] process > FreebayesSingle (SRR7062654... [ 8%] 61 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [6e/aaecbd] process > HaplotypeCaller (SRR7062654... [ 13%] 95 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 95 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3e/876243] process > FreebayesSingle (SRR7062654... [ 8%] 61 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1756) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [83/8267e4] process > HaplotypeCaller (SRR7062654... [ 14%] 101 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 101 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3e/876243] process > FreebayesSingle (SRR7062654... [ 8%] 61 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1759) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [78/cd716b] process > HaplotypeCaller (SRR7062654... [ 14%] 101 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 101 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3e/876243] process > FreebayesSingle (SRR7062654... [ 8%] 61 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1761) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [4b/b0350f] process > HaplotypeCaller (SRR7062654... [ 14%] 105 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 105 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [64/734ec7] process > FreebayesSingle (SRR7062654... [ 8%] 62 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1764) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [ed/bb76b7] process > HaplotypeCaller (SRR7062654... [ 14%] 105 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 105 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [64/734ec7] process > FreebayesSingle (SRR7062654... [ 8%] 62 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1767) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [e9/07e115] process > HaplotypeCaller (SRR7062654... [ 15%] 108 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 108 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [64/734ec7] process > FreebayesSingle (SRR7062654... [ 8%] 62 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1771) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [a3/5f335b] process > HaplotypeCaller (SRR7062654... [ 15%] 112 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 112 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [64/734ec7] process > FreebayesSingle (SRR7062654... [ 8%] 62 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1771) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [a3/5f335b] process > HaplotypeCaller (SRR7062654... [ 15%] 112 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 112 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9b/f58ca0] process > FreebayesSingle (SRR7062654... [ 9%] 63 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1777) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [43/00b738] process > HaplotypeCaller (SRR7062654... [ 16%] 117 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 117 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9b/f58ca0] process > FreebayesSingle (SRR7062654... [ 9%] 63 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1777) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [2b/0bd377] process > HaplotypeCaller (SRR7062654... [ 16%] 117 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 117 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9b/f58ca0] process > FreebayesSingle (SRR7062654... [ 9%] 63 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1777) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [65/0241a3] process > HaplotypeCaller (SRR7062654... [ 16%] 120 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 119 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9b/f58ca0] process > FreebayesSingle (SRR7062654... [ 9%] 63 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1781) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [d1/1e5f78] process > HaplotypeCaller (SRR7062654... [ 16%] 122 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 122 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9b/f58ca0] process > FreebayesSingle (SRR7062654... [ 9%] 63 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1782) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [32/c88e65] process > HaplotypeCaller (SRR7062654... [ 16%] 122 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 122 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9b/f58ca0] process > FreebayesSingle (SRR7062654... [ 9%] 63 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1782) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [32/c88e65] process > HaplotypeCaller (SRR7062654... [ 16%] 122 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 122 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9b/f58ca0] process > FreebayesSingle (SRR7062654... [ 9%] 63 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1783) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [25/1a0345] process > HaplotypeCaller (SRR7062654... [ 17%] 129 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 129 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9b/f58ca0] process > FreebayesSingle (SRR7062654... [ 9%] 63 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1788) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [79/8d880f] process > HaplotypeCaller (SRR7062654... [ 17%] 129 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 129 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9b/f58ca0] process > FreebayesSingle (SRR7062654... [ 9%] 63 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1789) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [40/300847] process > HaplotypeCaller (SRR7062654... [ 17%] 129 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 129 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9b/f58ca0] process > FreebayesSingle (SRR7062654... [ 9%] 63 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1789) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [32/d341cd] process > HaplotypeCaller (SRR7062654... [ 18%] 130 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 130 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9b/f58ca0] process > FreebayesSingle (SRR7062654... [ 9%] 63 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1791) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [cb/df2067] process > HaplotypeCaller (SRR7062654... [ 18%] 131 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 131 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9b/f58ca0] process > FreebayesSingle (SRR7062654... [ 9%] 63 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1791) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [9b/d5e100] process > HaplotypeCaller (SRR7062654... [ 18%] 132 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 132 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ca/34e4ec] process > FreebayesSingle (SRR7062654... [ 9%] 64 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1795) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [de/204375] process > HaplotypeCaller (SRR7062654... [ 18%] 134 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 134 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ca/34e4ec] process > FreebayesSingle (SRR7062654... [ 9%] 64 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1796) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [d9/2cabde] process > HaplotypeCaller (SRR7062654... [ 18%] 136 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 136 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ca/34e4ec] process > FreebayesSingle (SRR7062654... [ 9%] 64 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1797) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [0e/020f6a] process > HaplotypeCaller (SRR7062654... [ 18%] 136 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 136 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ca/34e4ec] process > FreebayesSingle (SRR7062654... [ 9%] 64 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1798) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [83/8267e4] process > HaplotypeCaller (SRR7062654... [ 19%] 142 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 141 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ca/34e4ec] process > FreebayesSingle (SRR7062654... [ 9%] 64 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1804) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [d1/cdab36] process > HaplotypeCaller (SRR7062654... [ 20%] 145 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 145 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ca/34e4ec] process > FreebayesSingle (SRR7062654... [ 9%] 64 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1806) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [95/269616] process > HaplotypeCaller (SRR7062654... [ 20%] 145 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 145 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ca/34e4ec] process > FreebayesSingle (SRR7062654... [ 9%] 64 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1808) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [b9/4afb75] process > HaplotypeCaller (SRR7062654... [ 21%] 158 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 157 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ca/34e4ec] process > FreebayesSingle (SRR7062654... [ 9%] 64 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1813) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [59/2d9d2b] process > HaplotypeCaller (SRR7062654... [ 21%] 158 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 158 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ca/34e4ec] process > FreebayesSingle (SRR7062654... [ 9%] 64 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1819) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [6e/91a057] process > HaplotypeCaller (SRR7062654... [ 21%] 158 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 158 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ca/34e4ec] process > FreebayesSingle (SRR7062654... [ 9%] 64 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1819) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [32/4eeadc] process > HaplotypeCaller (SRR7062654... [ 21%] 159 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 158 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ca/34e4ec] process > FreebayesSingle (SRR7062654... [ 9%] 64 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1822) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [0c/15740b] process > HaplotypeCaller (SRR7062654... [ 23%] 170 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 170 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ca/34e4ec] process > FreebayesSingle (SRR7062654... [ 9%] 64 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1828) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [0c/9a37c5] process > HaplotypeCaller (SRR7062654... [ 23%] 170 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 170 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ca/34e4ec] process > FreebayesSingle (SRR7062654... [ 9%] 64 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1831) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [ea/74e2fc] process > HaplotypeCaller (SRR7062654... [ 23%] 170 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 170 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ca/34e4ec] process > FreebayesSingle (SRR7062654... [ 9%] 64 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1831) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [af/18df82] process > HaplotypeCaller (SRR7062654... [ 24%] 175 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 174 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ca/34e4ec] process > FreebayesSingle (SRR7062654... [ 9%] 64 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1836) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [61/3cc2e4] process > HaplotypeCaller (SRR7062654... [ 24%] 175 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 175 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ca/34e4ec] process > FreebayesSingle (SRR7062654... [ 9%] 64 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1837) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [b9/a63599] process > HaplotypeCaller (SRR7062654... [ 24%] 178 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 178 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ca/34e4ec] process > FreebayesSingle (SRR7062654... [ 9%] 64 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1839) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [5c/bea1fb] process > HaplotypeCaller (SRR7062654... [ 24%] 178 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 178 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ca/34e4ec] process > FreebayesSingle (SRR7062654... [ 9%] 64 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1840) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [2f/72e854] process > HaplotypeCaller (SRR7062654... [ 24%] 179 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 179 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ca/34e4ec] process > FreebayesSingle (SRR7062654... [ 9%] 64 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1841) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [cb/df2067] process > HaplotypeCaller (SRR7062654... [ 25%] 186 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 186 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ca/34e4ec] process > FreebayesSingle (SRR7062654... [ 9%] 64 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1847) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [72/4f6df2] process > HaplotypeCaller (SRR7062654... [ 25%] 186 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 186 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ca/34e4ec] process > FreebayesSingle (SRR7062654... [ 9%] 64 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1848) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [95/269616] process > HaplotypeCaller (SRR7062654... [ 26%] 194 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 193 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ca/34e4ec] process > FreebayesSingle (SRR7062654... [ 9%] 64 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1852) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [5f/91ad13] process > HaplotypeCaller (SRR7062654... [ 26%] 194 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 194 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ca/34e4ec] process > FreebayesSingle (SRR7062654... [ 9%] 64 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1855) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [42/23d673] process > HaplotypeCaller (SRR7062654... [ 26%] 194 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 194 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ca/34e4ec] process > FreebayesSingle (SRR7062654... [ 9%] 64 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1858) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [4c/c726f1] process > HaplotypeCaller (SRR7062654... [ 27%] 200 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 200 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ca/34e4ec] process > FreebayesSingle (SRR7062654... [ 9%] 64 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1861) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [61/1f4df3] process > HaplotypeCaller (SRR7062654... [ 27%] 200 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 200 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ca/34e4ec] process > FreebayesSingle (SRR7062654... [ 9%] 64 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1864) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [a6/60a686] process > HaplotypeCaller (SRR7062654... [ 27%] 203 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 203 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ca/34e4ec] process > FreebayesSingle (SRR7062654... [ 9%] 64 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1866) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [d4/3a04a9] process > HaplotypeCaller (SRR7062654... [ 28%] 205 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 205 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ca/34e4ec] process > FreebayesSingle (SRR7062654... [ 9%] 64 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1869) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [c1/a397e8] process > HaplotypeCaller (SRR7062654... [ 28%] 207 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 207 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/0408c4] process > FreebayesSingle (SRR7062654... [ 9%] 65 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1869) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [25/1a0345] process > HaplotypeCaller (SRR7062654... [ 28%] 208 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 208 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/0408c4] process > FreebayesSingle (SRR7062654... [ 9%] 65 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1874) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [10/dcf15c] process > HaplotypeCaller (SRR7062654... [ 29%] 218 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 218 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/0408c4] process > FreebayesSingle (SRR7062654... [ 9%] 65 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1880) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [78/55065f] process > HaplotypeCaller (SRR7062654... [ 29%] 218 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 218 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/0408c4] process > FreebayesSingle (SRR7062654... [ 9%] 65 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1880) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [43/223584] process > HaplotypeCaller (SRR7062654... [ 30%] 221 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 221 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/0408c4] process > FreebayesSingle (SRR7062654... [ 9%] 65 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1884) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [2b/920b90] process > HaplotypeCaller (SRR7062654... [ 31%] 231 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 231 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/0408c4] process > FreebayesSingle (SRR7062654... [ 9%] 65 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1890) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [f3/c44d55] process > HaplotypeCaller (SRR7062654... [ 31%] 231 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 231 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/0408c4] process > FreebayesSingle (SRR7062654... [ 9%] 65 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1893) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [d8/4f8fd6] process > HaplotypeCaller (SRR7062654... [ 31%] 231 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 231 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/0408c4] process > FreebayesSingle (SRR7062654... [ 9%] 65 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1897) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [dc/96e6a8] process > HaplotypeCaller (SRR7062654... [ 32%] 234 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 234 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5b/357826] process > FreebayesSingle (SRR7062654... [ 9%] 66 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1900) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [d2/5851bb] process > HaplotypeCaller (SRR7062654... [ 33%] 242 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 242 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [42/b224c3] process > FreebayesSingle (SRR7062654... [ 9%] 66 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1905) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [d2/5851bb] process > HaplotypeCaller (SRR7062654... [ 33%] 242 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 242 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [50/928008] process > FreebayesSingle (SRR7062654... [ 9%] 66 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1909) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [a5/b138a2] process > HaplotypeCaller (SRR7062654... [ 33%] 246 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 246 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7a/e90e33] process > FreebayesSingle (SRR7062654... [ 9%] 66 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1909) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [ca/a01940] process > HaplotypeCaller (SRR7062654... [ 33%] 247 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 246 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7a/e90e33] process > FreebayesSingle (SRR7062654... [ 9%] 66 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1915) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [7d/829265] process > HaplotypeCaller (SRR7062654... [ 34%] 252 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 252 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7a/e90e33] process > FreebayesSingle (SRR7062654... [ 9%] 66 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1915) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [2d/3ec355] process > HaplotypeCaller (SRR7062654... [ 35%] 256 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 255 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7a/e90e33] process > FreebayesSingle (SRR7062654... [ 9%] 66 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1920) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [3e/42ee91] process > HaplotypeCaller (SRR7062654... [ 35%] 257 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 257 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e6/517d29] process > FreebayesSingle (SRR7062654... [ 9%] 66 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1920) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [61/1f4df3] process > HaplotypeCaller (SRR7062654... [ 36%] 263 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 263 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e6/517d29] process > FreebayesSingle (SRR7062654... [ 9%] 66 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1924) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [28/7cc6df] process > HaplotypeCaller (SRR7062654... [ 36%] 264 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 264 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e6/517d29] process > FreebayesSingle (SRR7062654... [ 9%] 66 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1927) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [28/7cc6df] process > HaplotypeCaller (SRR7062654... [ 36%] 264 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 264 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [74/49ee05] process > FreebayesSingle (SRR7062654... [ 9%] 66 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1928) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [27/92f457] process > HaplotypeCaller (SRR7062654... [ 37%] 272 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 272 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [bf/7fdc0a] process > FreebayesSingle (SRR7062654... [ 9%] 66 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1934) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [45/934582] process > HaplotypeCaller (SRR7062654... [ 37%] 275 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 275 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b7/15b85b] process > FreebayesSingle (SRR7062654... [ 9%] 66 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1938) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [45/934582] process > HaplotypeCaller (SRR7062654... [ 37%] 275 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 275 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [12/18de7e] process > FreebayesSingle (SRR7062654... [ 9%] 66 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1941) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [ad/1a66ca] process > HaplotypeCaller (SRR7062654... [ 38%] 283 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 283 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ed/bafb40] process > FreebayesSingle (SRR7062654... [ 9%] 66 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1947) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [ad/1a66ca] process > HaplotypeCaller (SRR7062654... [ 38%] 283 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 283 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [1f/cdcaab] process > FreebayesSingle (SRR7062654... [ 9%] 67 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1948) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [9c/935641] process > HaplotypeCaller (SRR7062654... [ 38%] 284 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 284 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0e/e162fb] process > FreebayesSingle (SRR7062654... [ 9%] 67 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1952) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [a8/a4d622] process > HaplotypeCaller (SRR7062654... [ 39%] 288 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 288 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [aa/a3d0fc] process > FreebayesSingle (SRR7062654... [ 9%] 67 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1954) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [7d/829265] process > HaplotypeCaller (SRR7062654... [ 40%] 296 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 296 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [40/e2666e] process > FreebayesSingle (SRR7062654... [ 9%] 69 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1960) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [7d/829265] process > HaplotypeCaller (SRR7062654... [ 40%] 296 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 296 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [72/8ec5fd] process > FreebayesSingle (SRR7062654... [ 9%] 69 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1962) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [7d/829265] process > HaplotypeCaller (SRR7062654... [ 40%] 296 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 296 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/d909b2] process > FreebayesSingle (SRR7062654... [ 9%] 69 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1964) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [34/be1edc] process > HaplotypeCaller (SRR7062654... [ 40%] 298 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 298 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3e/7655c8] process > FreebayesSingle (SRR7062654... [ 9%] 70 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1965) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [34/be1edc] process > HaplotypeCaller (SRR7062654... [ 40%] 298 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 298 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [1e/7794ca] process > FreebayesSingle (SRR7062654... [ 9%] 70 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1969) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [d8/4f8fd6] process > HaplotypeCaller (SRR7062654... [ 41%] 303 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 303 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [22/761803] process > FreebayesSingle (SRR7062654... [ 11%] 78 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1975) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [d8/4f8fd6] process > HaplotypeCaller (SRR7062654... [ 41%] 303 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 303 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [55/f553db] process > FreebayesSingle (SRR7062654... [ 11%] 78 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1978) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [d8/4f8fd6] process > HaplotypeCaller (SRR7062654... [ 41%] 303 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 303 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [d3/4d96fc] process > FreebayesSingle (SRR7062654... [ 11%] 78 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1978) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [5b/02cee7] process > HaplotypeCaller (SRR7062654... [ 41%] 304 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 304 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [d3/4d96fc] process > FreebayesSingle (SRR7062654... [ 11%] 78 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1984) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [d8/771c14] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 2 of 4 [cc/82fc93] process > HaplotypeCaller (SRR7062654... [ 42%] 309 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 309 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [c2/78ff40] process > FreebayesSingle (SRR7062654... [ 13%] 98 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1989) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [cc/82fc93] process > HaplotypeCaller (SRR7062654... [ 42%] 309 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 309 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [87/741f8e] process > FreebayesSingle (SRR7062654... [ 14%] 102 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [28/a9747d] process > Mpileup (SRR7062654-3_1-111... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (1995) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [cc/82fc93] process > HaplotypeCaller (SRR7062654... [ 42%] 309 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 309 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [87/741f8e] process > FreebayesSingle (SRR7062654... [ 14%] 102 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c9/e914ad] process > Mpileup (SRR7062654-16_1-65... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2001) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [cc/82fc93] process > HaplotypeCaller (SRR7062654... [ 42%] 309 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 309 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [87/741f8e] process > FreebayesSingle (SRR7062654... [ 14%] 102 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [dd/1013b4] process > Mpileup (SRR7062654-KQ75951... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2007) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [cc/82fc93] process > HaplotypeCaller (SRR7062654... [ 42%] 309 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 309 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [87/741f8e] process > FreebayesSingle (SRR7062654... [ 14%] 102 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b9/204a42] process > Mpileup (SRR7062654-AADN040... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2008) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [cc/82fc93] process > HaplotypeCaller (SRR7062654... [ 42%] 309 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 309 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [87/741f8e] process > FreebayesSingle (SRR7062654... [ 14%] 102 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7d/36506c] process > Mpileup (SRR7062654-AADN040... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2011) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [cc/82fc93] process > HaplotypeCaller (SRR7062654... [ 42%] 309 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 309 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [94/58ffd8] process > FreebayesSingle (SRR7062654... [ 14%] 106 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6d/dcb8dc] process > Mpileup (SRR7062654-AADN040... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2012) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [cc/82fc93] process > HaplotypeCaller (SRR7062654... [ 42%] 309 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 309 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [94/58ffd8] process > FreebayesSingle (SRR7062654... [ 14%] 106 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8b/c30465] process > Mpileup (SRR7062654-AADN040... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2014) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [10/dcf15c] process > HaplotypeCaller (SRR7062654... [ 42%] 310 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 310 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [97/485eb1] process > FreebayesSingle (SRR7062654... [ 14%] 107 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b0/4caf5b] process > Mpileup (SRR7062654-AADN040... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2016) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [bd/787546] process > HaplotypeCaller (SRR7062654... [ 42%] 312 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 312 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [97/485eb1] process > FreebayesSingle (SRR7062654... [ 14%] 107 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [74/de9402] process > Mpileup (SRR7062654-AADN040... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2019) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [28/7cc6df] process > HaplotypeCaller (SRR7062654... [ 43%] 316 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 316 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [97/485eb1] process > FreebayesSingle (SRR7062654... [ 14%] 107 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [63/b803eb] process > Mpileup (SRR7062654-AADN040... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2020) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [28/7cc6df] process > HaplotypeCaller (SRR7062654... [ 43%] 316 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 316 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [97/485eb1] process > FreebayesSingle (SRR7062654... [ 14%] 107 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [0b/324cfd] process > Mpileup (SRR7062654-AADN040... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2020) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [28/7cc6df] process > HaplotypeCaller (SRR7062654... [ 43%] 316 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 316 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [97/485eb1] process > FreebayesSingle (SRR7062654... [ 14%] 107 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [0b/324cfd] process > Mpileup (SRR7062654-AADN040... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2024) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [a2/defef8] process > HaplotypeCaller (SRR7062654... [ 43%] 317 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 317 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [95/2cb8fd] process > FreebayesSingle (SRR7062654... [ 15%] 111 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d2/47cf39] process > Mpileup (SRR7062654-AADN040... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2025) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [a2/defef8] process > HaplotypeCaller (SRR7062654... [ 43%] 317 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 317 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [95/2cb8fd] process > FreebayesSingle (SRR7062654... [ 15%] 111 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2a/a81aa6] process > Mpileup (SRR7062654-AADN040... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2028) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [f3/c44d55] process > HaplotypeCaller (SRR7062654... [ 43%] 318 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 318 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [63/d36057] process > FreebayesSingle (SRR7062654... [ 17%] 127 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [78/1ab703] process > Mpileup (SRR7062654-AADN040... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2033) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [f3/c44d55] process > HaplotypeCaller (SRR7062654... [ 43%] 318 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 318 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [87/741f8e] process > FreebayesSingle (SRR7062654... [ 17%] 129 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fe/9b3573] process > Mpileup (SRR7062654-AADN040... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2039) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [f3/c44d55] process > HaplotypeCaller (SRR7062654... [ 43%] 318 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 318 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [87/741f8e] process > FreebayesSingle (SRR7062654... [ 17%] 129 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1a/05385c] process > Mpileup (SRR7062654-AADN040... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2044) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [f3/c44d55] process > HaplotypeCaller (SRR7062654... [ 43%] 318 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 318 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [87/741f8e] process > FreebayesSingle (SRR7062654... [ 17%] 129 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [90/216e2d] process > Mpileup (SRR7062654-AADN040... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2047) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [78/55065f] process > HaplotypeCaller (SRR7062654... [ 43%] 319 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 319 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9f/13af66] process > FreebayesSingle (SRR7062654... [ 18%] 131 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [55/3d812f] process > Mpileup (SRR7062654-AADN040... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2048) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [d7/bbf2c9] process > HaplotypeCaller (SRR7062654... [ 43%] 320 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 320 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9f/13af66] process > FreebayesSingle (SRR7062654... [ 18%] 131 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c8/67c57b] process > Mpileup (SRR7062654-KQ75943... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2048) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [d7/bbf2c9] process > HaplotypeCaller (SRR7062654... [ 43%] 320 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 320 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9f/13af66] process > FreebayesSingle (SRR7062654... [ 18%] 131 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c8/67c57b] process > Mpileup (SRR7062654-KQ75943... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2048) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [d7/bbf2c9] process > HaplotypeCaller (SRR7062654... [ 43%] 320 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 320 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9f/13af66] process > FreebayesSingle (SRR7062654... [ 18%] 131 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c8/67c57b] process > Mpileup (SRR7062654-KQ75943... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2048) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [d7/bbf2c9] process > HaplotypeCaller (SRR7062654... [ 43%] 320 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 320 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [22/761803] process > FreebayesSingle (SRR7062654... [ 18%] 133 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c8/67c57b] process > Mpileup (SRR7062654-KQ75943... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2050) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [d7/bbf2c9] process > HaplotypeCaller (SRR7062654... [ 43%] 320 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 320 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [22/761803] process > FreebayesSingle (SRR7062654... [ 18%] 133 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [39/66c26c] process > Mpileup (SRR7062654-AADN040... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2050) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [d7/bbf2c9] process > HaplotypeCaller (SRR7062654... [ 43%] 320 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 320 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [22/761803] process > FreebayesSingle (SRR7062654... [ 18%] 133 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [39/66c26c] process > Mpileup (SRR7062654-AADN040... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2051) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [46/82febe] process > HaplotypeCaller (SRR7062654... [ 43%] 321 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 321 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [22/761803] process > FreebayesSingle (SRR7062654... [ 18%] 133 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [06/b279d6] process > Mpileup (SRR7062654-AADN040... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2052) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [46/82febe] process > HaplotypeCaller (SRR7062654... [ 43%] 321 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 321 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [8b/afa782] process > FreebayesSingle (SRR7062654... [ 18%] 134 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ac/128f35] process > Mpileup (SRR7062654-AADN040... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2052) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [46/82febe] process > HaplotypeCaller (SRR7062654... [ 43%] 321 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 321 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [8b/afa782] process > FreebayesSingle (SRR7062654... [ 18%] 134 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ac/128f35] process > Mpileup (SRR7062654-AADN040... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2053) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [46/82febe] process > HaplotypeCaller (SRR7062654... [ 43%] 321 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 321 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7a/e90e33] process > FreebayesSingle (SRR7062654... [ 18%] 135 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [3e/c15e03] process > Mpileup (SRR7062654-AADN040... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2053) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [46/82febe] process > HaplotypeCaller (SRR7062654... [ 43%] 321 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 321 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7a/e90e33] process > FreebayesSingle (SRR7062654... [ 18%] 135 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [3e/c15e03] process > Mpileup (SRR7062654-AADN040... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2054) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [46/82febe] process > HaplotypeCaller (SRR7062654... [ 43%] 321 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 321 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4b/9e350e] process > FreebayesSingle (SRR7062654... [ 18%] 136 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [98/144894] process > Mpileup (SRR7062654-AADN040... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2055) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [46/82febe] process > HaplotypeCaller (SRR7062654... [ 43%] 321 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 321 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2a/9b3580] process > FreebayesSingle (SRR7062654... [ 19%] 137 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6a/995049] process > Mpileup (SRR7062654-AADN040... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2055) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [46/82febe] process > HaplotypeCaller (SRR7062654... [ 43%] 321 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 321 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2a/9b3580] process > FreebayesSingle (SRR7062654... [ 19%] 137 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6a/995049] process > Mpileup (SRR7062654-AADN040... [ 0%] 0 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2057) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [46/82febe] process > HaplotypeCaller (SRR7062654... [ 43%] 321 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 321 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2a/9b3580] process > FreebayesSingle (SRR7062654... [ 19%] 137 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d1/cc602f] process > Mpileup (SRR7062654-AADN040... [ 0%] 2 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2058) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [46/82febe] process > HaplotypeCaller (SRR7062654... [ 43%] 321 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 321 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2a/9b3580] process > FreebayesSingle (SRR7062654... [ 19%] 137 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9e/4f0728] process > Mpileup (SRR7062654-AADN040... [ 0%] 3 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2058) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [46/82febe] process > HaplotypeCaller (SRR7062654... [ 43%] 321 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 321 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2a/9b3580] process > FreebayesSingle (SRR7062654... [ 19%] 137 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9e/4f0728] process > Mpileup (SRR7062654-AADN040... [ 0%] 3 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2059) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [46/82febe] process > HaplotypeCaller (SRR7062654... [ 43%] 321 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 321 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2a/9b3580] process > FreebayesSingle (SRR7062654... [ 19%] 137 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a8/636c2c] process > Mpileup (SRR7062654-AADN040... [ 1%] 4 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2059) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [46/82febe] process > HaplotypeCaller (SRR7062654... [ 43%] 321 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 321 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2a/9b3580] process > FreebayesSingle (SRR7062654... [ 19%] 137 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a1/1c2552] process > Mpileup (SRR7062654-AADN040... [ 1%] 5 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2062) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [46/82febe] process > HaplotypeCaller (SRR7062654... [ 43%] 321 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 321 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2a/9b3580] process > FreebayesSingle (SRR7062654... [ 19%] 137 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a8/2e18e5] process > Mpileup (SRR7062654-AADN040... [ 1%] 7 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2062) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [46/82febe] process > HaplotypeCaller (SRR7062654... [ 43%] 321 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 321 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2a/9b3580] process > FreebayesSingle (SRR7062654... [ 19%] 137 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [30/3168fa] process > Mpileup (SRR7062654-AADN040... [ 1%] 8 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2064) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [46/82febe] process > HaplotypeCaller (SRR7062654... [ 43%] 321 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 321 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2a/9b3580] process > FreebayesSingle (SRR7062654... [ 19%] 137 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [3f/f058fb] process > Mpileup (SRR7062654-AADN040... [ 1%] 10 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2065) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [46/82febe] process > HaplotypeCaller (SRR7062654... [ 43%] 321 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 321 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2a/9b3580] process > FreebayesSingle (SRR7062654... [ 19%] 137 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ff/69d3b8] process > Mpileup (SRR7062654-AADN040... [ 1%] 10 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2066) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [46/82febe] process > HaplotypeCaller (SRR7062654... [ 43%] 321 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 321 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2a/9b3580] process > FreebayesSingle (SRR7062654... [ 19%] 137 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6e/709cd3] process > Mpileup (SRR7062654-AADN040... [ 1%] 11 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2068) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [46/82febe] process > HaplotypeCaller (SRR7062654... [ 43%] 321 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 321 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [dd/eb4f5c] process > FreebayesSingle (SRR7062654... [ 19%] 138 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/2484c5] process > Mpileup (SRR7062654-AADN040... [ 2%] 12 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2069) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [46/82febe] process > HaplotypeCaller (SRR7062654... [ 43%] 321 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 321 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [dd/eb4f5c] process > FreebayesSingle (SRR7062654... [ 19%] 138 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9e/ae634d] process > Mpileup (SRR7062654-AADN040... [ 2%] 13 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2070) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [46/82febe] process > HaplotypeCaller (SRR7062654... [ 43%] 321 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 321 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [dd/eb4f5c] process > FreebayesSingle (SRR7062654... [ 19%] 138 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [51/9c223d] process > Mpileup (SRR7062654-AADN040... [ 2%] 14 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2070) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [46/82febe] process > HaplotypeCaller (SRR7062654... [ 43%] 321 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 321 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [dd/eb4f5c] process > FreebayesSingle (SRR7062654... [ 19%] 138 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [51/9c223d] process > Mpileup (SRR7062654-AADN040... [ 2%] 14 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2071) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [46/82febe] process > HaplotypeCaller (SRR7062654... [ 43%] 321 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 321 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [dd/eb4f5c] process > FreebayesSingle (SRR7062654... [ 19%] 138 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8d/890346] process > Mpileup (SRR7062654-AADN040... [ 2%] 15 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2072) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [46/82febe] process > HaplotypeCaller (SRR7062654... [ 43%] 321 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 321 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [dd/eb4f5c] process > FreebayesSingle (SRR7062654... [ 19%] 138 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c8/b7927f] process > Mpileup (SRR7062654-AADN040... [ 2%] 16 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2074) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [54/93327a] process > HaplotypeCaller (SRR7062654... [ 44%] 322 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 322 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [dd/eb4f5c] process > FreebayesSingle (SRR7062654... [ 19%] 138 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a0/49b789] process > Mpileup (SRR7062654-AADN040... [ 2%] 17 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2075) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [54/93327a] process > HaplotypeCaller (SRR7062654... [ 44%] 322 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 322 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [dd/eb4f5c] process > FreebayesSingle (SRR7062654... [ 19%] 138 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d6/d74dc7] process > Mpileup (SRR7062654-AADN040... [ 2%] 18 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2076) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [54/93327a] process > HaplotypeCaller (SRR7062654... [ 44%] 322 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 322 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [dd/eb4f5c] process > FreebayesSingle (SRR7062654... [ 19%] 138 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [eb/9ea8d5] process > Mpileup (SRR7062654-AADN040... [ 3%] 19 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2078) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [54/93327a] process > HaplotypeCaller (SRR7062654... [ 44%] 322 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 322 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [dd/eb4f5c] process > FreebayesSingle (SRR7062654... [ 19%] 138 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [86/cd68aa] process > Mpileup (SRR7062654-AADN040... [ 3%] 21 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2078) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [54/93327a] process > HaplotypeCaller (SRR7062654... [ 44%] 322 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 322 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [dd/eb4f5c] process > FreebayesSingle (SRR7062654... [ 19%] 138 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1b/f54593] process > Mpileup (SRR7062654-AADN040... [ 3%] 22 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2079) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [54/93327a] process > HaplotypeCaller (SRR7062654... [ 44%] 322 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 322 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [dd/eb4f5c] process > FreebayesSingle (SRR7062654... [ 19%] 138 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [58/a4b058] process > Mpileup (SRR7062654-AADN040... [ 3%] 22 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2079) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [46/fe2dec] process > HaplotypeCaller (SRR7062654... [ 44%] 323 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 323 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [35/eccf81] process > FreebayesSingle (SRR7062654... [ 19%] 140 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [58/a4b058] process > Mpileup (SRR7062654-AADN040... [ 3%] 22 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2083) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [46/fe2dec] process > HaplotypeCaller (SRR7062654... [ 44%] 323 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 323 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [35/eccf81] process > FreebayesSingle (SRR7062654... [ 19%] 140 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1d/5b7e21] process > Mpileup (SRR7062654-AADN040... [ 3%] 23 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2084) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 323 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [35/eccf81] process > FreebayesSingle (SRR7062654... [ 19%] 140 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [e9/0f48cf] process > Mpileup (SRR7062654-AADN040... [ 3%] 23 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2085) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [35/eccf81] process > FreebayesSingle (SRR7062654... [ 19%] 140 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [e5/d373c5] process > Mpileup (SRR7062654-AADN040... [ 3%] 23 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2086) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [35/eccf81] process > FreebayesSingle (SRR7062654... [ 19%] 140 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d4/e09fc5] process > Mpileup (SRR7062654-AADN040... [ 3%] 25 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2087) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [35/eccf81] process > FreebayesSingle (SRR7062654... [ 19%] 140 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8e/c9e4f8] process > Mpileup (SRR7062654-AADN040... [ 3%] 25 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2088) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [35/eccf81] process > FreebayesSingle (SRR7062654... [ 19%] 140 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a5/5db732] process > Mpileup (SRR7062654-AADN040... [ 4%] 28 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2090) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [35/eccf81] process > FreebayesSingle (SRR7062654... [ 19%] 140 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [89/743114] process > Mpileup (SRR7062654-AADN040... [ 4%] 28 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2091) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [35/eccf81] process > FreebayesSingle (SRR7062654... [ 19%] 140 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [87/cefe43] process > Mpileup (SRR7062654-AADN040... [ 4%] 29 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2092) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [35/eccf81] process > FreebayesSingle (SRR7062654... [ 19%] 140 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [66/2e9a60] process > Mpileup (SRR7062654-AADN040... [ 4%] 30 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2093) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [35/eccf81] process > FreebayesSingle (SRR7062654... [ 19%] 140 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8b/0e4eda] process > Mpileup (SRR7062654-AADN040... [ 4%] 31 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2093) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [35/eccf81] process > FreebayesSingle (SRR7062654... [ 19%] 140 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8b/0e4eda] process > Mpileup (SRR7062654-AADN040... [ 4%] 31 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2094) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [35/eccf81] process > FreebayesSingle (SRR7062654... [ 19%] 140 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ae/92f9dc] process > Mpileup (SRR7062654-AADN040... [ 4%] 32 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2097) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [42/b224c3] process > FreebayesSingle (SRR7062654... [ 19%] 141 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [08/3d3636] process > Mpileup (SRR7062654-AADN040... [ 5%] 34 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2099) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [fd/735ec4] process > FreebayesSingle (SRR7062654... [ 19%] 142 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [98/90c499] process > Mpileup (SRR7062654-AADN040... [ 5%] 35 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2099) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [fd/735ec4] process > FreebayesSingle (SRR7062654... [ 19%] 142 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [98/90c499] process > Mpileup (SRR7062654-AADN040... [ 5%] 35 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2101) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [fd/735ec4] process > FreebayesSingle (SRR7062654... [ 19%] 142 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [24/dd1bd8] process > Mpileup (SRR7062654-AADN040... [ 5%] 37 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2103) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [fd/735ec4] process > FreebayesSingle (SRR7062654... [ 19%] 142 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c8/df6496] process > Mpileup (SRR7062654-AADN040... [ 5%] 39 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2104) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [fd/735ec4] process > FreebayesSingle (SRR7062654... [ 19%] 142 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [14/2c4f15] process > Mpileup (SRR7062654-AADN040... [ 5%] 40 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2107) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [fd/735ec4] process > FreebayesSingle (SRR7062654... [ 19%] 142 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [af/ad03b0] process > Mpileup (SRR7062654-AADN040... [ 6%] 43 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2109) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [fd/735ec4] process > FreebayesSingle (SRR7062654... [ 19%] 142 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [21/df25de] process > Mpileup (SRR7062654-AADN040... [ 6%] 45 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2109) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [fd/735ec4] process > FreebayesSingle (SRR7062654... [ 19%] 142 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [08/cfd6b0] process > Mpileup (SRR7062654-KQ75954... [ 6%] 46 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2111) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [fd/735ec4] process > FreebayesSingle (SRR7062654... [ 19%] 142 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [36/43884c] process > Mpileup (SRR7062654-AADN040... [ 7%] 51 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2115) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [fd/735ec4] process > FreebayesSingle (SRR7062654... [ 19%] 142 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ae/1fa85e] process > Mpileup (SRR7062654-AADN040... [ 7%] 51 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2115) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ae/1fa85e] process > Mpileup (SRR7062654-AADN040... [ 7%] 51 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2116) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b8/2b348d] process > Mpileup (SRR7062654-AADN040... [ 7%] 51 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2117) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1e/f818b1] process > Mpileup (SRR7062654-AADN040... [ 7%] 53 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2118) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [0f/54198a] process > Mpileup (SRR7062654-AADN040... [ 7%] 53 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2119) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [50/a806d6] process > Mpileup (SRR7062654-AADN040... [ 7%] 55 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2120) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [68/34f54f] process > Mpileup (SRR7062654-AADN040... [ 7%] 55 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2122) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [99/ae1da3] process > Mpileup (SRR7062654-AADN040... [ 8%] 57 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2122) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c8/1c6f7d] process > Mpileup (SRR7062654-AADN040... [ 8%] 57 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2124) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a9/5e4cca] process > Mpileup (SRR7062654-AADN040... [ 8%] 61 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2126) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [09/da4248] process > Mpileup (SRR7062654-AADN040... [ 8%] 61 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2128) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [37/77da04] process > Mpileup (SRR7062654-AADN040... [ 9%] 64 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2129) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fe/a17dff] process > Mpileup (SRR7062654-AADN040... [ 9%] 64 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2130) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/3c057e] process > Mpileup (SRR7062654-AADN040... [ 9%] 65 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2131) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [69/dbf097] process > Mpileup (SRR7062654-AADN040... [ 9%] 66 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2132) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [95/e04678] process > Mpileup (SRR7062654-AADN040... [ 9%] 67 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2132) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [95/e04678] process > Mpileup (SRR7062654-AADN040... [ 9%] 67 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2133) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b1/f33d31] process > Mpileup (SRR7062654-KQ75948... [ 9%] 68 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2135) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [01/9c6f01] process > Mpileup (SRR7062654-AADN040... [ 9%] 70 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2136) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [01/a470c7] process > Mpileup (SRR7062654-KQ75962... [ 10%] 71 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2136) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [01/a470c7] process > Mpileup (SRR7062654-KQ75962... [ 10%] 71 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2137) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b4/0a03fd] process > Mpileup (SRR7062654-AADN040... [ 10%] 72 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2138) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [bf/7ea2ec] process > Mpileup (SRR7062654-AADN040... [ 10%] 73 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2138) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [bf/7ea2ec] process > Mpileup (SRR7062654-AADN040... [ 10%] 73 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2138) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d1/cc602f] process > Mpileup (SRR7062654-AADN040... [ 10%] 74 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2139) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [23/a8f97f] process > Mpileup (SRR7062654-AADN040... [ 10%] 74 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2139) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [51/9c223d] process > Mpileup (SRR7062654-AADN040... [ 10%] 75 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2141) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c7/34ad09] process > Mpileup (SRR7062654-AADN040... [ 10%] 76 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2142) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [e1/03411f] process > Mpileup (SRR7062654-AADN040... [ 10%] 77 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2143) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [79/396cdf] process > Mpileup (SRR7062654-AADN040... [ 11%] 78 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2144) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [03/0f7fd4] process > Mpileup (SRR7062654-AADN040... [ 11%] 79 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2145) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d6/83c86a] process > Mpileup (SRR7062654-AADN040... [ 11%] 80 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2147) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f5/a64549] process > Mpileup (SRR7062654-AADN040... [ 11%] 82 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2147) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f5/a64549] process > Mpileup (SRR7062654-AADN040... [ 11%] 82 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2148) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [68/427456] process > HaplotypeCaller (SRR7062654... [ 44%] 324 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 324 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [51/9ab973] process > Mpileup (SRR7062654-AADN040... [ 11%] 83 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2149) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2c/72ccdb] process > Mpileup (SRR7062654-AADN040... [ 11%] 83 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2150) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b8/79e996] process > Mpileup (SRR7062654-AADN040... [ 11%] 84 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2151) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cf/c595de] process > Mpileup (SRR7062654-AADN040... [ 11%] 85 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2153) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [42/c4a235] process > Mpileup (SRR7062654-AADN040... [ 12%] 87 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2153) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [42/c4a235] process > Mpileup (SRR7062654-AADN040... [ 12%] 87 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2154) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d6/045638] process > Mpileup (SRR7062654-AADN040... [ 12%] 88 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2155) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [e0/253297] process > Mpileup (SRR7062654-AADN040... [ 12%] 89 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2156) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [40/cf8a10] process > Mpileup (SRR7062654-AADN040... [ 12%] 90 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2156) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [46/6b07ab] process > Mpileup (SRR7062654-AADN040... [ 12%] 91 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2157) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [3e/0878cb] process > Mpileup (SRR7062654-AADN040... [ 12%] 91 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2158) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [09/f5c83d] process > Mpileup (SRR7062654-AADN040... [ 12%] 92 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2159) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ea/82a3d7] process > Mpileup (SRR7062654-KQ75957... [ 13%] 94 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2160) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c0/7c610c] process > Mpileup (SRR7062654-AADN040... [ 13%] 94 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2161) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c8/9912cd] process > Mpileup (SRR7062654-KQ75967... [ 13%] 95 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2162) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c5/93f8a8] process > Mpileup (SRR7062654-AADN040... [ 13%] 96 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2163) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [40/f43f7f] process > Mpileup (SRR7062654-AADN040... [ 13%] 98 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2164) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [74/80ed17] process > Mpileup (SRR7062654-AADN040... [ 13%] 98 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2166) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/0fc7bd] process > Mpileup (SRR7062654-AADN040... [ 14%] 101 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2167) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [bf/220d95] process > Mpileup (SRR7062654-AADN040... [ 14%] 101 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2169) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [e3/0371b7] process > Mpileup (SRR7062654-AADN040... [ 14%] 104 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2170) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [aa/a6dc97] process > Mpileup (SRR7062654-AADN040... [ 14%] 104 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2172) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [53/3f25dd] process > Mpileup (SRR7062654-AADN040... [ 14%] 106 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2173) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [de/22ed61] process > Mpileup (SRR7062654-AADN040... [ 14%] 107 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2174) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cb/b71675] process > Mpileup (SRR7062654-AADN040... [ 15%] 108 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2178) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d1/dd2f09] process > Mpileup (SRR7062654-AADN040... [ 15%] 112 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2179) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6a/704903] process > Mpileup (SRR7062654-AADN040... [ 15%] 113 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2182) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/704b2b] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [17/f7370a] process > Mpileup (SRR7062654-AADN040... [ 16%] 116 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2183) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9c/61ea79] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d6/d74dc7] process > Mpileup (SRR7062654-AADN040... [ 16%] 117 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2183) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9c/61ea79] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b4/0a03fd] process > Mpileup (SRR7062654-AADN040... [ 16%] 118 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2184) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ba/47fbb1] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b4/0a03fd] process > Mpileup (SRR7062654-AADN040... [ 16%] 118 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2185) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [26/bbb116] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [74/4acabd] process > Mpileup (SRR7062654-AADN040... [ 16%] 119 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2185) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [26/bbb116] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [bf/7ea2ec] process > Mpileup (SRR7062654-AADN040... [ 17%] 123 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2189) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e2/4fbb33] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cb/52b351] process > Mpileup (SRR7062654-9_1-240... [ 17%] 123 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2189) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e2/4fbb33] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cb/52b351] process > Mpileup (SRR7062654-9_1-240... [ 17%] 123 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2189) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e2/4fbb33] process > FreebayesSingle (SRR7062654... [ 19%] 143 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cb/52b351] process > Mpileup (SRR7062654-9_1-240... [ 17%] 123 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2190) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [08/dfbd5e] process > FreebayesSingle (SRR7062654... [ 20%] 145 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cb/52b351] process > Mpileup (SRR7062654-9_1-240... [ 17%] 123 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2191) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [52/644e37] process > FreebayesSingle (SRR7062654... [ 20%] 145 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cb/52b351] process > Mpileup (SRR7062654-9_1-240... [ 17%] 123 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2193) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [30/dea924] process > FreebayesSingle (SRR7062654... [ 20%] 148 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [60/d4e01f] process > Mpileup (SRR7062654-AADN040... [ 17%] 124 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2195) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c3/f9f7c9] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a2/3748d8] process > FreebayesSingle (SRR7062654... [ 20%] 148 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [60/d4e01f] process > Mpileup (SRR7062654-AADN040... [ 17%] 124 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2197) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [cd/a8fd7a] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e8/d62e7a] process > FreebayesSingle (SRR7062654... [ 20%] 149 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [14/2c4f15] process > Mpileup (SRR7062654-AADN040... [ 17%] 125 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2201) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [e6/537beb] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e8/d62e7a] process > FreebayesSingle (SRR7062654... [ 20%] 149 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [69/dbf097] process > Mpileup (SRR7062654-AADN040... [ 18%] 130 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2202) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [ba/45ee73] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e8/d62e7a] process > FreebayesSingle (SRR7062654... [ 20%] 149 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [69/dbf097] process > Mpileup (SRR7062654-AADN040... [ 18%] 130 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2204) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [fe/31a2cd] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e8/d62e7a] process > FreebayesSingle (SRR7062654... [ 20%] 149 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [e1/03411f] process > Mpileup (SRR7062654-AADN040... [ 18%] 132 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2207) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [9e/4ba0e1] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e8/d62e7a] process > FreebayesSingle (SRR7062654... [ 20%] 151 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d5/5f252c] process > Mpileup (SRR7062654-KQ75960... [ 18%] 133 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2211) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [40/7aa1a3] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a2/3748d8] process > FreebayesSingle (SRR7062654... [ 21%] 156 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [13/78af44] process > Mpileup (SRR7062654-AADN040... [ 18%] 134 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2213) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [15/b2351f] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a2/3748d8] process > FreebayesSingle (SRR7062654... [ 21%] 156 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [13/78af44] process > Mpileup (SRR7062654-AADN040... [ 18%] 134 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2215) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [5a/049a10] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a2/3748d8] process > FreebayesSingle (SRR7062654... [ 21%] 156 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [79/396cdf] process > Mpileup (SRR7062654-AADN040... [ 18%] 136 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2215) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [5a/049a10] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a2/3748d8] process > FreebayesSingle (SRR7062654... [ 21%] 156 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [79/396cdf] process > Mpileup (SRR7062654-AADN040... [ 18%] 136 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2215) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [5a/049a10] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a2/3748d8] process > FreebayesSingle (SRR7062654... [ 21%] 156 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [79/396cdf] process > Mpileup (SRR7062654-AADN040... [ 18%] 136 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2215) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [5a/049a10] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a2/3748d8] process > FreebayesSingle (SRR7062654... [ 21%] 156 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c8/1c6f7d] process > Mpileup (SRR7062654-AADN040... [ 19%] 138 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2217) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [7a/cd86b5] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a2/3748d8] process > FreebayesSingle (SRR7062654... [ 21%] 156 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c8/1c6f7d] process > Mpileup (SRR7062654-AADN040... [ 19%] 138 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2218) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [8d/20cba5] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a2/3748d8] process > FreebayesSingle (SRR7062654... [ 21%] 156 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [86/7936bb] process > Mpileup (SRR7062654-AADN040... [ 19%] 139 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2219) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c6/c4f1a7] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a2/3748d8] process > FreebayesSingle (SRR7062654... [ 21%] 156 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [99/ae1da3] process > Mpileup (SRR7062654-AADN040... [ 19%] 141 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2220) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [e9/89c40d] process > HaplotypeCaller (SRR7062654... [ 44%] 325 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 325 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a2/3748d8] process > FreebayesSingle (SRR7062654... [ 21%] 156 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [99/ae1da3] process > Mpileup (SRR7062654-AADN040... [ 19%] 141 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2220) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [15/b2351f] process > HaplotypeCaller (SRR7062654... [ 44%] 328 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 327 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a2/3748d8] process > FreebayesSingle (SRR7062654... [ 21%] 156 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [99/ae1da3] process > Mpileup (SRR7062654-AADN040... [ 19%] 141 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2223) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [1d/eaf105] process > HaplotypeCaller (SRR7062654... [ 44%] 328 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 328 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a2/3748d8] process > FreebayesSingle (SRR7062654... [ 21%] 156 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [99/ae1da3] process > Mpileup (SRR7062654-AADN040... [ 19%] 141 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2226) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [fb/368002] process > HaplotypeCaller (SRR7062654... [ 44%] 329 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 329 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [bc/ea6de9] process > FreebayesSingle (SRR7062654... [ 21%] 156 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ae/1fa85e] process > Mpileup (SRR7062654-AADN040... [ 19%] 143 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2229) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [9e/f76806] process > HaplotypeCaller (SRR7062654... [ 45%] 330 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 330 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [71/0f4aad] process > FreebayesSingle (SRR7062654... [ 21%] 156 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b1/f33d31] process > Mpileup (SRR7062654-KQ75948... [ 20%] 145 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2232) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [94/335e99] process > HaplotypeCaller (SRR7062654... [ 45%] 333 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 333 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [43/efa02d] process > FreebayesSingle (SRR7062654... [ 21%] 156 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/3c057e] process > Mpileup (SRR7062654-AADN040... [ 20%] 146 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2233) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [94/335e99] process > HaplotypeCaller (SRR7062654... [ 45%] 333 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 333 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [d9/c97c7b] process > FreebayesSingle (SRR7062654... [ 21%] 156 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/3c057e] process > Mpileup (SRR7062654-AADN040... [ 20%] 146 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2235) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [8d/20cba5] process > HaplotypeCaller (SRR7062654... [ 45%] 335 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 335 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ab/029a23] process > FreebayesSingle (SRR7062654... [ 21%] 156 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/3c057e] process > Mpileup (SRR7062654-AADN040... [ 20%] 146 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2237) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [c9/adbd47] process > HaplotypeCaller (SRR7062654... [ 45%] 336 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 336 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [83/debae3] process > FreebayesSingle (SRR7062654... [ 21%] 157 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/3c057e] process > Mpileup (SRR7062654-AADN040... [ 20%] 146 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2241) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [34/eb7083] process > HaplotypeCaller (SRR7062654... [ 46%] 338 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 338 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [1e/c5941a] process > FreebayesSingle (SRR7062654... [ 22%] 162 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/3c057e] process > Mpileup (SRR7062654-AADN040... [ 20%] 146 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2244) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [34/eb7083] process > HaplotypeCaller (SRR7062654... [ 46%] 338 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 338 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [38/f825b2] process > FreebayesSingle (SRR7062654... [ 22%] 162 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/3c057e] process > Mpileup (SRR7062654-AADN040... [ 20%] 146 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2245) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [e4/6182f5] process > HaplotypeCaller (SRR7062654... [ 46%] 339 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 339 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6a/24570f] process > FreebayesSingle (SRR7062654... [ 22%] 162 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/3c057e] process > Mpileup (SRR7062654-AADN040... [ 20%] 146 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2247) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [5a/049a10] process > HaplotypeCaller (SRR7062654... [ 46%] 340 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 340 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5f/1b6c3e] process > FreebayesSingle (SRR7062654... [ 22%] 162 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c7/34ad09] process > Mpileup (SRR7062654-AADN040... [ 20%] 147 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2247) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [cb/d8b858] process > HaplotypeCaller (SRR7062654... [ 46%] 341 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 340 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5f/1b6c3e] process > FreebayesSingle (SRR7062654... [ 22%] 162 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c7/34ad09] process > Mpileup (SRR7062654-AADN040... [ 20%] 147 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2249) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [1d/eaf105] process > HaplotypeCaller (SRR7062654... [ 46%] 342 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 342 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [70/547385] process > FreebayesSingle (SRR7062654... [ 22%] 162 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c7/34ad09] process > Mpileup (SRR7062654-AADN040... [ 20%] 147 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2250) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [1d/eaf105] process > HaplotypeCaller (SRR7062654... [ 46%] 342 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 342 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [51/21a1db] process > FreebayesSingle (SRR7062654... [ 22%] 165 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c7/34ad09] process > Mpileup (SRR7062654-AADN040... [ 20%] 147 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2252) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [1d/eaf105] process > HaplotypeCaller (SRR7062654... [ 46%] 342 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 342 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [c9/926c6a] process > FreebayesSingle (SRR7062654... [ 22%] 165 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c7/34ad09] process > Mpileup (SRR7062654-AADN040... [ 20%] 147 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2253) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [94/335e99] process > HaplotypeCaller (SRR7062654... [ 46%] 343 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 343 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [1c/e199d5] process > FreebayesSingle (SRR7062654... [ 23%] 171 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c7/34ad09] process > Mpileup (SRR7062654-AADN040... [ 20%] 147 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2260) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [94/335e99] process > HaplotypeCaller (SRR7062654... [ 46%] 343 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 343 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [dc/ceb6a6] process > FreebayesSingle (SRR7062654... [ 24%] 175 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c7/34ad09] process > Mpileup (SRR7062654-AADN040... [ 20%] 147 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2263) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [94/335e99] process > HaplotypeCaller (SRR7062654... [ 46%] 343 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 343 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [fd/822df9] process > FreebayesSingle (SRR7062654... [ 24%] 175 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c7/34ad09] process > Mpileup (SRR7062654-AADN040... [ 20%] 147 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2264) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [9e/4ba0e1] process > HaplotypeCaller (SRR7062654... [ 46%] 344 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 344 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [79/463f58] process > FreebayesSingle (SRR7062654... [ 24%] 175 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c7/34ad09] process > Mpileup (SRR7062654-AADN040... [ 20%] 147 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2265) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [9e/4ba0e1] process > HaplotypeCaller (SRR7062654... [ 46%] 344 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 344 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3f/8e6e9b] process > FreebayesSingle (SRR7062654... [ 24%] 175 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2e/f5dd06] process > Mpileup (SRR7062654-AADN040... [ 20%] 148 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2265) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [9e/4ba0e1] process > HaplotypeCaller (SRR7062654... [ 46%] 344 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 344 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3f/8e6e9b] process > FreebayesSingle (SRR7062654... [ 24%] 175 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2e/f5dd06] process > Mpileup (SRR7062654-AADN040... [ 20%] 148 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2269) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [53/adf922] process > HaplotypeCaller (SRR7062654... [ 47%] 345 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 345 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [11/d9e645] process > FreebayesSingle (SRR7062654... [ 24%] 177 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [bf/220c1d] process > Mpileup (SRR7062654-W_1-516... [ 20%] 150 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2270) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [53/adf922] process > HaplotypeCaller (SRR7062654... [ 47%] 345 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 345 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [11/d9e645] process > FreebayesSingle (SRR7062654... [ 24%] 177 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b4/b4d35e] process > Mpileup (SRR7062654-26_1-53... [ 20%] 150 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2273) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [34/eb7083] process > HaplotypeCaller (SRR7062654... [ 47%] 346 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 346 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [73/dfafa4] process > FreebayesSingle (SRR7062654... [ 26%] 190 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [e7/4732db] process > Mpileup (SRR7062654-28_1-49... [ 20%] 151 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2277) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [34/eb7083] process > HaplotypeCaller (SRR7062654... [ 47%] 346 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 346 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [21/8900be] process > FreebayesSingle (SRR7062654... [ 26%] 191 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ef/6d1d7b] process > Mpileup (SRR7062654-25_1-29... [ 20%] 151 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2283) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [34/eb7083] process > HaplotypeCaller (SRR7062654... [ 47%] 346 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 346 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [21/8900be] process > FreebayesSingle (SRR7062654... [ 26%] 191 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [54/74fc40] process > Mpileup (SRR7062654-AADN040... [ 20%] 151 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2286) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [34/eb7083] process > HaplotypeCaller (SRR7062654... [ 47%] 346 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 346 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [21/8900be] process > FreebayesSingle (SRR7062654... [ 26%] 191 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [84/b90e4c] process > Mpileup (SRR7062654-AADN040... [ 20%] 151 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2289) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [34/eb7083] process > HaplotypeCaller (SRR7062654... [ 47%] 346 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 346 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3f/8e6e9b] process > FreebayesSingle (SRR7062654... [ 26%] 193 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ae/1b233d] process > Mpileup (SRR7062654-AADN040... [ 21%] 152 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2291) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [34/eb7083] process > HaplotypeCaller (SRR7062654... [ 47%] 346 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 346 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3f/8e6e9b] process > FreebayesSingle (SRR7062654... [ 26%] 193 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f9/a14745] process > Mpileup (SRR7062654-AADN040... [ 21%] 154 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2291) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [34/eb7083] process > HaplotypeCaller (SRR7062654... [ 47%] 346 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 346 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3f/8e6e9b] process > FreebayesSingle (SRR7062654... [ 26%] 193 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [bf/220d95] process > Mpileup (SRR7062654-AADN040... [ 21%] 155 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2293) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [34/eb7083] process > HaplotypeCaller (SRR7062654... [ 47%] 346 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 346 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3f/8e6e9b] process > FreebayesSingle (SRR7062654... [ 26%] 193 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d0/725c9b] process > Mpileup (SRR7062654-AADN040... [ 21%] 156 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2293) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [34/eb7083] process > HaplotypeCaller (SRR7062654... [ 47%] 346 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 346 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3f/8e6e9b] process > FreebayesSingle (SRR7062654... [ 26%] 193 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d0/725c9b] process > Mpileup (SRR7062654-AADN040... [ 21%] 156 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2293) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [34/eb7083] process > HaplotypeCaller (SRR7062654... [ 47%] 346 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 346 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3f/8e6e9b] process > FreebayesSingle (SRR7062654... [ 26%] 193 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d0/725c9b] process > Mpileup (SRR7062654-AADN040... [ 21%] 156 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2294) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [34/eb7083] process > HaplotypeCaller (SRR7062654... [ 47%] 346 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 346 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [11/d9e645] process > FreebayesSingle (SRR7062654... [ 26%] 194 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [68/a7f431] process > Mpileup (SRR7062654-AADN040... [ 21%] 158 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2296) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [34/eb7083] process > HaplotypeCaller (SRR7062654... [ 47%] 346 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 346 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [11/d9e645] process > FreebayesSingle (SRR7062654... [ 26%] 194 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [25/74e472] process > Mpileup (SRR7062654-AADN040... [ 21%] 158 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2297) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [34/eb7083] process > HaplotypeCaller (SRR7062654... [ 47%] 346 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 346 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [21/8900be] process > FreebayesSingle (SRR7062654... [ 27%] 200 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c1/790566] process > Mpileup (SRR7062654-AADN040... [ 21%] 158 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2302) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [34/eb7083] process > HaplotypeCaller (SRR7062654... [ 47%] 346 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 346 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [21/8900be] process > FreebayesSingle (SRR7062654... [ 27%] 200 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [93/f9b7f8] process > Mpileup (SRR7062654-AADN040... [ 21%] 158 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2304) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [ac/c749f8] process > HaplotypeCaller (SRR7062654... [ 47%] 347 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 347 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7a/c2db37] process > FreebayesSingle (SRR7062654... [ 27%] 201 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [34/6f06d4] process > Mpileup (SRR7062654-AADN040... [ 21%] 158 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2306) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [ac/c749f8] process > HaplotypeCaller (SRR7062654... [ 47%] 347 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 347 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5d/a5af58] process > FreebayesSingle (SRR7062654... [ 27%] 201 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [eb/bd97dd] process > Mpileup (SRR7062654-AADN040... [ 22%] 161 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2307) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [ac/c749f8] process > HaplotypeCaller (SRR7062654... [ 47%] 347 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 347 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5d/a5af58] process > FreebayesSingle (SRR7062654... [ 27%] 201 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [89/831b23] process > Mpileup (SRR7062654-24_1-62... [ 22%] 161 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2308) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [ac/c749f8] process > HaplotypeCaller (SRR7062654... [ 47%] 347 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 347 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5d/a5af58] process > FreebayesSingle (SRR7062654... [ 27%] 201 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [97/219588] process > Mpileup (SRR7062654-18_1-11... [ 22%] 162 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2310) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [ac/c749f8] process > HaplotypeCaller (SRR7062654... [ 47%] 347 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 347 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5d/a5af58] process > FreebayesSingle (SRR7062654... [ 27%] 201 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d0/e7fef1] process > Mpileup (SRR7062654-20_1-14... [ 22%] 165 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2311) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [ac/c749f8] process > HaplotypeCaller (SRR7062654... [ 47%] 347 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 347 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5d/a5af58] process > FreebayesSingle (SRR7062654... [ 27%] 201 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [61/7d699c] process > Mpileup (SRR7062654-23_1-57... [ 22%] 165 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2312) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [fe/31a2cd] process > HaplotypeCaller (SRR7062654... [ 47%] 348 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 348 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5d/a5af58] process > FreebayesSingle (SRR7062654... [ 27%] 201 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [de/f7ed95] process > Mpileup (SRR7062654-12_1-19... [ 22%] 165 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2314) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [fe/31a2cd] process > HaplotypeCaller (SRR7062654... [ 47%] 348 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 348 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5d/a5af58] process > FreebayesSingle (SRR7062654... [ 27%] 202 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [87/460e27] process > Mpileup (SRR7062654-21_1-68... [ 22%] 166 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2316) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [fe/31a2cd] process > HaplotypeCaller (SRR7062654... [ 47%] 348 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 348 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5d/a5af58] process > FreebayesSingle (SRR7062654... [ 27%] 202 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [42/5e7b39] process > Mpileup (SRR7062654-6_1-354... [ 23%] 168 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2317) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [fe/31a2cd] process > HaplotypeCaller (SRR7062654... [ 47%] 348 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 348 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5d/a5af58] process > FreebayesSingle (SRR7062654... [ 27%] 202 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ef/4cf321] process > Mpileup (SRR7062654-13_1-18... [ 23%] 169 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2318) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [fe/31a2cd] process > HaplotypeCaller (SRR7062654... [ 47%] 348 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 348 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5d/a5af58] process > FreebayesSingle (SRR7062654... [ 27%] 202 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [03/e39513] process > Mpileup (SRR7062654-5_1-598... [ 23%] 170 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2318) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [fe/31a2cd] process > HaplotypeCaller (SRR7062654... [ 47%] 348 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 348 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5d/a5af58] process > FreebayesSingle (SRR7062654... [ 27%] 202 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [03/e39513] process > Mpileup (SRR7062654-5_1-598... [ 23%] 170 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2318) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [fe/31a2cd] process > HaplotypeCaller (SRR7062654... [ 47%] 348 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 348 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5d/a5af58] process > FreebayesSingle (SRR7062654... [ 27%] 202 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [58/bd3add] process > Mpileup (SRR7062654-AADN040... [ 23%] 171 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2319) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [fe/31a2cd] process > HaplotypeCaller (SRR7062654... [ 47%] 348 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 348 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5d/a5af58] process > FreebayesSingle (SRR7062654... [ 27%] 202 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [4a/688190] process > Mpileup (SRR7062654-27_1-56... [ 23%] 171 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2319) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [fe/31a2cd] process > HaplotypeCaller (SRR7062654... [ 47%] 348 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 348 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5d/a5af58] process > FreebayesSingle (SRR7062654... [ 27%] 202 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [e0/253297] process > Mpileup (SRR7062654-AADN040... [ 23%] 172 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2320) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [fe/31a2cd] process > HaplotypeCaller (SRR7062654... [ 47%] 348 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 348 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5d/a5af58] process > FreebayesSingle (SRR7062654... [ 27%] 202 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ed/cc467d] process > Mpileup (SRR7062654-17_1-10... [ 23%] 172 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2321) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [fe/31a2cd] process > HaplotypeCaller (SRR7062654... [ 47%] 348 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 348 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5d/a5af58] process > FreebayesSingle (SRR7062654... [ 27%] 202 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7f/0b3171] process > Mpileup (SRR7062654-15_1-12... [ 23%] 173 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2322) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [fe/31a2cd] process > HaplotypeCaller (SRR7062654... [ 47%] 348 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 348 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5d/a5af58] process > FreebayesSingle (SRR7062654... [ 27%] 202 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [34/aeb50a] process > Mpileup (SRR7062654-14_1-15... [ 24%] 174 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2322) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [e7/55d602] process > HaplotypeCaller (SRR7062654... [ 47%] 349 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 349 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5d/a5af58] process > FreebayesSingle (SRR7062654... [ 27%] 202 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [34/aeb50a] process > Mpileup (SRR7062654-14_1-15... [ 24%] 174 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2323) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [e7/55d602] process > HaplotypeCaller (SRR7062654... [ 47%] 349 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 349 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5d/a5af58] process > FreebayesSingle (SRR7062654... [ 27%] 202 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2d/79199c] process > Mpileup (SRR7062654-7_1-369... [ 24%] 174 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2324) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [e7/55d602] process > HaplotypeCaller (SRR7062654... [ 47%] 349 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 349 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5d/a5af58] process > FreebayesSingle (SRR7062654... [ 27%] 202 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [44/07fe30] process > Mpileup (SRR7062654-10_1-20... [ 24%] 177 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2326) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [e7/55d602] process > HaplotypeCaller (SRR7062654... [ 47%] 349 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 349 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5d/a5af58] process > FreebayesSingle (SRR7062654... [ 27%] 202 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [39/11d6a6] process > Mpileup (SRR7062654-4_1-912... [ 24%] 177 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2327) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [e7/55d602] process > HaplotypeCaller (SRR7062654... [ 47%] 349 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 349 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5d/a5af58] process > FreebayesSingle (SRR7062654... [ 27%] 202 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [08/a226a5] process > Mpileup (SRR7062654-AADN040... [ 24%] 178 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2329) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [e7/55d602] process > HaplotypeCaller (SRR7062654... [ 47%] 349 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 349 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [8d/867a55] process > FreebayesSingle (SRR7062654... [ 27%] 202 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ae/0e1f1e] process > Mpileup (SRR7062654-AADN040... [ 24%] 181 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2330) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [e7/55d602] process > HaplotypeCaller (SRR7062654... [ 47%] 349 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 349 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [8d/867a55] process > FreebayesSingle (SRR7062654... [ 27%] 202 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ef/31efea] process > Mpileup (SRR7062654-AADN040... [ 24%] 181 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2332) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [e7/55d602] process > HaplotypeCaller (SRR7062654... [ 47%] 349 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 349 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [71/0f4aad] process > FreebayesSingle (SRR7062654... [ 27%] 203 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [54/be8634] process > Mpileup (SRR7062654-AADN040... [ 25%] 182 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2333) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [e7/55d602] process > HaplotypeCaller (SRR7062654... [ 47%] 349 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 349 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e3/0b6229] process > FreebayesSingle (SRR7062654... [ 28%] 204 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [05/63c0fd] process > Mpileup (SRR7062654-AADN040... [ 25%] 182 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2334) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [e7/55d602] process > HaplotypeCaller (SRR7062654... [ 47%] 349 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 349 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [8d/867a55] process > FreebayesSingle (SRR7062654... [ 28%] 205 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [4d/5005a5] process > Mpileup (SRR7062654-AADN040... [ 25%] 182 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2336) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [e7/55d602] process > HaplotypeCaller (SRR7062654... [ 47%] 349 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 349 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [8d/867a55] process > FreebayesSingle (SRR7062654... [ 28%] 205 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/05775d] process > Mpileup (SRR7062654-AADN040... [ 25%] 184 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2338) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [e7/55d602] process > HaplotypeCaller (SRR7062654... [ 47%] 349 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 349 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [8d/867a55] process > FreebayesSingle (SRR7062654... [ 28%] 205 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [37/8d9fba] process > Mpileup (SRR7062654-AADN040... [ 25%] 186 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2338) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [e7/55d602] process > HaplotypeCaller (SRR7062654... [ 47%] 349 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 349 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [8d/867a55] process > FreebayesSingle (SRR7062654... [ 28%] 205 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [37/8d9fba] process > Mpileup (SRR7062654-AADN040... [ 25%] 186 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2340) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [e7/55d602] process > HaplotypeCaller (SRR7062654... [ 47%] 349 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 349 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [29/1bbe30] process > FreebayesSingle (SRR7062654... [ 28%] 205 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [17/f7370a] process > Mpileup (SRR7062654-AADN040... [ 25%] 188 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2341) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e3/358bfb] process > FreebayesSingle (SRR7062654... [ 28%] 205 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [17/f7370a] process > Mpileup (SRR7062654-AADN040... [ 25%] 188 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2343) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [c9/e03862] process > FreebayesSingle (SRR7062654... [ 28%] 205 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6a/704903] process > Mpileup (SRR7062654-AADN040... [ 26%] 190 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2345) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [96/c5c9bc] process > FreebayesSingle (SRR7062654... [ 28%] 207 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6a/704903] process > Mpileup (SRR7062654-AADN040... [ 26%] 190 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2347) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [60/769a5e] process > FreebayesSingle (SRR7062654... [ 28%] 209 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b8/fe45aa] process > Mpileup (SRR7062654-AADN040... [ 26%] 190 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2347) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [60/769a5e] process > FreebayesSingle (SRR7062654... [ 28%] 209 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b8/fe45aa] process > Mpileup (SRR7062654-AADN040... [ 26%] 190 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2347) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [60/769a5e] process > FreebayesSingle (SRR7062654... [ 28%] 209 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b8/fe45aa] process > Mpileup (SRR7062654-AADN040... [ 26%] 190 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2347) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [16/b0a048] process > FreebayesSingle (SRR7062654... [ 29%] 211 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b8/fe45aa] process > Mpileup (SRR7062654-AADN040... [ 26%] 190 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2350) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [98/e0f55c] process > FreebayesSingle (SRR7062654... [ 29%] 212 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b8/fe45aa] process > Mpileup (SRR7062654-AADN040... [ 26%] 190 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2352) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [cf/d0c943] process > FreebayesSingle (SRR7062654... [ 29%] 214 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b8/fe45aa] process > Mpileup (SRR7062654-AADN040... [ 26%] 190 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2353) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [db/4dbfce] process > FreebayesSingle (SRR7062654... [ 29%] 214 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [5e/74e165] process > Mpileup (SRR7062654-AADN040... [ 26%] 191 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2354) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2d/e84f07] process > FreebayesSingle (SRR7062654... [ 29%] 214 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [80/f25580] process > Mpileup (SRR7062654-AADN040... [ 26%] 192 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2355) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [c7/1cdd9b] process > FreebayesSingle (SRR7062654... [ 29%] 215 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [80/f25580] process > Mpileup (SRR7062654-AADN040... [ 26%] 192 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2358) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0c/df9b16] process > FreebayesSingle (SRR7062654... [ 29%] 218 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [80/f25580] process > Mpileup (SRR7062654-AADN040... [ 26%] 192 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2361) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [14/d9cb63] process > FreebayesSingle (SRR7062654... [ 30%] 222 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cf/5342ba] process > Mpileup (SRR7062654-AADN040... [ 26%] 193 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2363) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [90/609ef3] process > FreebayesSingle (SRR7062654... [ 30%] 222 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cf/5342ba] process > Mpileup (SRR7062654-AADN040... [ 26%] 193 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2364) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [90/609ef3] process > FreebayesSingle (SRR7062654... [ 30%] 222 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fd/9b0937] process > Mpileup (SRR7062654-AADN040... [ 26%] 194 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2366) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [d6/5739af] process > FreebayesSingle (SRR7062654... [ 30%] 222 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [e7/4732db] process > Mpileup (SRR7062654-28_1-49... [ 26%] 196 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2368) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e8/1dc76f] process > FreebayesSingle (SRR7062654... [ 31%] 229 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [34/6f06d4] process > Mpileup (SRR7062654-AADN040... [ 27%] 199 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2372) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [be/ac5707] process > FreebayesSingle (SRR7062654... [ 31%] 229 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [05/bf52e6] process > Mpileup (SRR7062654-AADN040... [ 27%] 199 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2376) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [98/013a10] process > FreebayesSingle (SRR7062654... [ 31%] 229 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [05/bf52e6] process > Mpileup (SRR7062654-AADN040... [ 27%] 199 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2378) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/9c11d9] process > FreebayesSingle (SRR7062654... [ 31%] 231 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a1/188d5a] process > Mpileup (SRR7062654-AADN040... [ 27%] 199 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2379) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [49/99683e] process > FreebayesSingle (SRR7062654... [ 31%] 231 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a1/188d5a] process > Mpileup (SRR7062654-AADN040... [ 27%] 199 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2380) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4f/256111] process > FreebayesSingle (SRR7062654... [ 31%] 231 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [eb/bd97dd] process > Mpileup (SRR7062654-AADN040... [ 27%] 200 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2380) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3a/51412b] process > FreebayesSingle (SRR7062654... [ 32%] 234 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [eb/bd97dd] process > Mpileup (SRR7062654-AADN040... [ 27%] 200 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2386) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/1e4fd7] process > FreebayesSingle (SRR7062654... [ 32%] 240 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [64/418dc3] process > Mpileup (SRR7062654-AADN040... [ 27%] 200 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2389) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ce/9ccaba] process > FreebayesSingle (SRR7062654... [ 32%] 240 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [64/418dc3] process > Mpileup (SRR7062654-AADN040... [ 27%] 200 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2389) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/9c11d9] process > FreebayesSingle (SRR7062654... [ 33%] 244 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [64/418dc3] process > Mpileup (SRR7062654-AADN040... [ 27%] 200 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2393) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/9c11d9] process > FreebayesSingle (SRR7062654... [ 33%] 244 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9f/db90c7] process > Mpileup (SRR7062654-AADN040... [ 27%] 200 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2394) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/9c11d9] process > FreebayesSingle (SRR7062654... [ 33%] 244 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d3/7d4be7] process > Mpileup (SRR7062654-AADN040... [ 27%] 201 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2394) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/9c11d9] process > FreebayesSingle (SRR7062654... [ 33%] 244 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d3/7d4be7] process > Mpileup (SRR7062654-AADN040... [ 27%] 201 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2394) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/9c11d9] process > FreebayesSingle (SRR7062654... [ 33%] 244 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d3/7d4be7] process > Mpileup (SRR7062654-AADN040... [ 27%] 201 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2396) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [bf/559590] process > FreebayesSingle (SRR7062654... [ 34%] 248 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [5b/da4f9d] process > Mpileup (SRR7062654-AADN040... [ 27%] 201 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2398) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [cf/775a4e] process > FreebayesSingle (SRR7062654... [ 34%] 248 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/b62a5c] process > Mpileup (SRR7062654-AADN040... [ 27%] 201 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2400) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/e9230b] process > FreebayesSingle (SRR7062654... [ 34%] 251 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/b62a5c] process > Mpileup (SRR7062654-AADN040... [ 27%] 201 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2401) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/e9230b] process > FreebayesSingle (SRR7062654... [ 34%] 251 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [bf/cc207c] process > Mpileup (SRR7062654-AADN040... [ 27%] 201 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2403) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/e9230b] process > FreebayesSingle (SRR7062654... [ 34%] 251 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1e/9c1850] process > Mpileup (SRR7062654-AADN040... [ 27%] 203 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2406) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [88/a1da36] process > FreebayesSingle (SRR7062654... [ 34%] 252 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [68/761c02] process > Mpileup (SRR7062654-AADN040... [ 28%] 205 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2408) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/179e7e] process > FreebayesSingle (SRR7062654... [ 34%] 255 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [02/68349c] process > Mpileup (SRR7062654-AADN040... [ 28%] 205 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2409) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7c/e51660] process > FreebayesSingle (SRR7062654... [ 34%] 255 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [02/68349c] process > Mpileup (SRR7062654-AADN040... [ 28%] 205 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2411) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [d2/5f5fcd] process > FreebayesSingle (SRR7062654... [ 34%] 255 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [96/457ecf] process > Mpileup (SRR7062654-AADN040... [ 28%] 207 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2412) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [d2/5f5fcd] process > FreebayesSingle (SRR7062654... [ 34%] 255 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [3f/3cb1ce] process > Mpileup (SRR7062654-AADN040... [ 28%] 208 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2415) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [ea/43a974] process > HaplotypeCaller (SRR7062654... [ 47%] 350 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 350 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7c/e51660] process > FreebayesSingle (SRR7062654... [ 35%] 256 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [10/500da0] process > Mpileup (SRR7062654-AADN040... [ 28%] 210 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2417) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [89/6ac497] process > FreebayesSingle (SRR7062654... [ 35%] 256 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fd/ed8429] process > Mpileup (SRR7062654-AADN040... [ 29%] 211 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2420) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6a/4ba5c6] process > FreebayesSingle (SRR7062654... [ 35%] 258 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7c/0fe1d5] process > Mpileup (SRR7062654-AADN040... [ 29%] 212 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2421) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6a/4ba5c6] process > FreebayesSingle (SRR7062654... [ 35%] 258 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f8/796a70] process > Mpileup (SRR7062654-AADN040... [ 29%] 213 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2423) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6a/65d864] process > FreebayesSingle (SRR7062654... [ 35%] 258 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ef/31efea] process > Mpileup (SRR7062654-AADN040... [ 29%] 215 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2424) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6a/65d864] process > FreebayesSingle (SRR7062654... [ 35%] 258 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ef/df3490] process > Mpileup (SRR7062654-AADN040... [ 29%] 216 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2426) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [75/b4c99c] process > FreebayesSingle (SRR7062654... [ 35%] 259 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [da/bbd7d2] process > Mpileup (SRR7062654-AADN040... [ 29%] 217 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2429) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [df/dbf1fe] process > FreebayesSingle (SRR7062654... [ 35%] 262 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ae/05a976] process > Mpileup (SRR7062654-AADN040... [ 29%] 217 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2429) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [df/dbf1fe] process > FreebayesSingle (SRR7062654... [ 35%] 262 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [97/219588] process > Mpileup (SRR7062654-18_1-11... [ 29%] 218 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2432) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [1f/548aa9] process > FreebayesSingle (SRR7062654... [ 36%] 264 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [64/7f5875] process > Mpileup (SRR7062654-AADN040... [ 29%] 218 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2432) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [1f/548aa9] process > FreebayesSingle (SRR7062654... [ 36%] 264 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d0/e7fef1] process > Mpileup (SRR7062654-20_1-14... [ 30%] 220 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2434) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [1f/548aa9] process > FreebayesSingle (SRR7062654... [ 36%] 264 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d3/376e36] process > Mpileup (SRR7062654-AADN040... [ 30%] 220 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2435) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [1f/548aa9] process > FreebayesSingle (SRR7062654... [ 36%] 264 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [81/5951dc] process > Mpileup (SRR7062654-AADN040... [ 30%] 221 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2436) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [1f/548aa9] process > FreebayesSingle (SRR7062654... [ 36%] 264 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [57/34cda9] process > Mpileup (SRR7062654-AADN040... [ 30%] 223 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2437) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [1f/548aa9] process > FreebayesSingle (SRR7062654... [ 36%] 264 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1f/209e31] process > Mpileup (SRR7062654-AADN040... [ 30%] 223 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2438) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [1f/548aa9] process > FreebayesSingle (SRR7062654... [ 36%] 265 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a4/2d1642] process > Mpileup (SRR7062654-AADN040... [ 30%] 225 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2440) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [1f/548aa9] process > FreebayesSingle (SRR7062654... [ 36%] 265 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [18/763de4] process > Mpileup (SRR7062654-AADN040... [ 30%] 225 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2442) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [df/dbf1fe] process > FreebayesSingle (SRR7062654... [ 36%] 267 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6a/d4b556] process > Mpileup (SRR7062654-AADN040... [ 30%] 225 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2443) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [df/dbf1fe] process > FreebayesSingle (SRR7062654... [ 36%] 267 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/f740a8] process > Mpileup (SRR7062654-AADN040... [ 31%] 226 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2444) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [df/dbf1fe] process > FreebayesSingle (SRR7062654... [ 36%] 267 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cf/6d7138] process > Mpileup (SRR7062654-AADN040... [ 31%] 227 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2446) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [df/dbf1fe] process > FreebayesSingle (SRR7062654... [ 36%] 267 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [74/870d44] process > Mpileup (SRR7062654-AADN040... [ 31%] 232 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2449) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [11/89a9b2] process > FreebayesSingle (SRR7062654... [ 36%] 267 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [63/56e66d] process > Mpileup (SRR7062654-AADN040... [ 31%] 232 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2450) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [11/89a9b2] process > FreebayesSingle (SRR7062654... [ 36%] 267 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [95/bad891] process > Mpileup (SRR7062654-AADN040... [ 31%] 233 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2451) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [11/89a9b2] process > FreebayesSingle (SRR7062654... [ 36%] 267 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [3f/d0f11c] process > Mpileup (SRR7062654-AADN040... [ 32%] 234 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2452) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [11/89a9b2] process > FreebayesSingle (SRR7062654... [ 36%] 268 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/df3856] process > Mpileup (SRR7062654-AADN040... [ 32%] 234 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2454) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4b/e28f25] process > FreebayesSingle (SRR7062654... [ 36%] 268 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6f/da1452] process > Mpileup (SRR7062654-AADN040... [ 32%] 236 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2454) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4b/e28f25] process > FreebayesSingle (SRR7062654... [ 36%] 268 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6f/da1452] process > Mpileup (SRR7062654-AADN040... [ 32%] 236 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2455) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4b/e28f25] process > FreebayesSingle (SRR7062654... [ 36%] 268 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f5/f744ef] process > Mpileup (SRR7062654-AADN040... [ 32%] 237 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2456) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4b/e28f25] process > FreebayesSingle (SRR7062654... [ 36%] 268 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/b1bcd5] process > Mpileup (SRR7062654-AADN040... [ 32%] 238 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2457) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4b/e28f25] process > FreebayesSingle (SRR7062654... [ 36%] 269 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [5b/0d2089] process > Mpileup (SRR7062654-AADN040... [ 32%] 238 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2458) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [aa/a955b3] process > HaplotypeCaller (SRR7062654... [ 47%] 351 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4b/e28f25] process > FreebayesSingle (SRR7062654... [ 36%] 269 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [95/ad995c] process > Mpileup (SRR7062654-AADN040... [ 32%] 239 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2458) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [e6/537beb] process > HaplotypeCaller (SRR7062654... [ 48%] 352 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 351 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4b/e28f25] process > FreebayesSingle (SRR7062654... [ 36%] 269 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [95/ad995c] process > Mpileup (SRR7062654-AADN040... [ 32%] 239 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2459) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [e6/537beb] process > HaplotypeCaller (SRR7062654... [ 48%] 352 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 352 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4b/e28f25] process > FreebayesSingle (SRR7062654... [ 36%] 269 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1a/164e7d] process > Mpileup (SRR7062654-AADN040... [ 32%] 239 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2459) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [e6/537beb] process > HaplotypeCaller (SRR7062654... [ 48%] 352 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 352 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4b/e28f25] process > FreebayesSingle (SRR7062654... [ 36%] 269 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a8/992cec] process > Mpileup (SRR7062654-11_1-20... [ 32%] 240 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2460) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [e6/537beb] process > HaplotypeCaller (SRR7062654... [ 48%] 352 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 352 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4b/e28f25] process > FreebayesSingle (SRR7062654... [ 36%] 269 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cb/38419c] process > Mpileup (SRR7062654-AADN040... [ 32%] 240 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2461) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [e6/537beb] process > HaplotypeCaller (SRR7062654... [ 48%] 352 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 352 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4b/e28f25] process > FreebayesSingle (SRR7062654... [ 36%] 269 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b1/c12b3e] process > Mpileup (SRR7062654-AADN040... [ 33%] 242 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2462) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [e6/537beb] process > HaplotypeCaller (SRR7062654... [ 48%] 352 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 352 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4b/e28f25] process > FreebayesSingle (SRR7062654... [ 36%] 269 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [63/63da77] process > Mpileup (SRR7062654-AADN040... [ 33%] 242 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2463) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [e6/537beb] process > HaplotypeCaller (SRR7062654... [ 48%] 352 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 352 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7c/47dbb6] process > FreebayesSingle (SRR7062654... [ 36%] 269 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9f/db90c7] process > Mpileup (SRR7062654-AADN040... [ 33%] 245 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2465) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [e6/537beb] process > HaplotypeCaller (SRR7062654... [ 48%] 352 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 352 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [c1/4e80ac] process > FreebayesSingle (SRR7062654... [ 36%] 269 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [eb/1db846] process > Mpileup (SRR7062654-AADN040... [ 33%] 245 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2465) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [e6/537beb] process > HaplotypeCaller (SRR7062654... [ 48%] 352 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 352 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [c1/4e80ac] process > FreebayesSingle (SRR7062654... [ 36%] 269 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [eb/1db846] process > Mpileup (SRR7062654-AADN040... [ 33%] 245 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2466) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [e6/537beb] process > HaplotypeCaller (SRR7062654... [ 48%] 352 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 352 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [c1/4e80ac] process > FreebayesSingle (SRR7062654... [ 36%] 270 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b2/4e47ad] process > Mpileup (SRR7062654-AADN040... [ 33%] 245 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2468) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [e6/537beb] process > HaplotypeCaller (SRR7062654... [ 48%] 352 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 352 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [8d/02f855] process > FreebayesSingle (SRR7062654... [ 37%] 271 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [64/418dc3] process > Mpileup (SRR7062654-AADN040... [ 33%] 246 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2469) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [e6/537beb] process > HaplotypeCaller (SRR7062654... [ 48%] 352 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 352 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [8d/02f855] process > FreebayesSingle (SRR7062654... [ 37%] 271 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [93/ff41e2] process > Mpileup (SRR7062654-AADN040... [ 33%] 247 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2471) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [e6/537beb] process > HaplotypeCaller (SRR7062654... [ 48%] 352 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 352 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ac/d5f3dc] process > FreebayesSingle (SRR7062654... [ 37%] 271 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [5a/0d2f66] process > Mpileup (SRR7062654-AADN040... [ 34%] 249 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2473) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [e6/537beb] process > HaplotypeCaller (SRR7062654... [ 48%] 352 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 352 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ac/d5f3dc] process > FreebayesSingle (SRR7062654... [ 37%] 271 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [5d/aa4678] process > Mpileup (SRR7062654-AADN040... [ 34%] 251 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2473) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [e6/537beb] process > HaplotypeCaller (SRR7062654... [ 48%] 352 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 352 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ac/d5f3dc] process > FreebayesSingle (SRR7062654... [ 37%] 271 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [5d/aa4678] process > Mpileup (SRR7062654-AADN040... [ 34%] 251 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2476) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [e6/537beb] process > HaplotypeCaller (SRR7062654... [ 48%] 352 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 352 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [86/252755] process > FreebayesSingle (SRR7062654... [ 37%] 274 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [90/08f0a7] process > Mpileup (SRR7062654-AADN040... [ 34%] 251 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2477) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [e6/537beb] process > HaplotypeCaller (SRR7062654... [ 48%] 352 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 352 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7e/98fbc8] process > FreebayesSingle (SRR7062654... [ 37%] 274 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7f/0b3171] process > Mpileup (SRR7062654-15_1-12... [ 34%] 252 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2479) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [8b/b58907] process > FreebayesSingle (SRR7062654... [ 37%] 274 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9e/b7e2a4] process > Mpileup (SRR7062654-AADN040... [ 34%] 253 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2480) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [8b/b58907] process > FreebayesSingle (SRR7062654... [ 37%] 274 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1d/07587e] process > Mpileup (SRR7062654-AADN040... [ 34%] 254 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2481) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [64/0eef7b] process > FreebayesSingle (SRR7062654... [ 37%] 274 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [02/68349c] process > Mpileup (SRR7062654-AADN040... [ 34%] 255 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2482) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f2/68c1bd] process > FreebayesSingle (SRR7062654... [ 37%] 275 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [02/68349c] process > Mpileup (SRR7062654-AADN040... [ 34%] 255 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2485) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5f/21e5f7] process > FreebayesSingle (SRR7062654... [ 37%] 277 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [dd/b8237a] process > Mpileup (SRR7062654-AADN040... [ 35%] 256 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2486) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5f/21e5f7] process > FreebayesSingle (SRR7062654... [ 37%] 277 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [bf/a37819] process > Mpileup (SRR7062654-AADN040... [ 35%] 257 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2487) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a0/d9c17b] process > FreebayesSingle (SRR7062654... [ 37%] 277 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [87/460e27] process > Mpileup (SRR7062654-21_1-68... [ 35%] 258 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2487) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a0/d9c17b] process > FreebayesSingle (SRR7062654... [ 37%] 277 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fd/ed8429] process > Mpileup (SRR7062654-AADN040... [ 35%] 259 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2488) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [58/8e7665] process > FreebayesSingle (SRR7062654... [ 37%] 277 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fd/ed8429] process > Mpileup (SRR7062654-AADN040... [ 35%] 259 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2488) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a0/d9c17b] process > FreebayesSingle (SRR7062654... [ 38%] 279 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fd/ed8429] process > Mpileup (SRR7062654-AADN040... [ 35%] 259 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2490) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/113ce9] process > FreebayesSingle (SRR7062654... [ 38%] 279 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fd/ed8429] process > Mpileup (SRR7062654-AADN040... [ 35%] 259 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2491) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [08/d68b5e] process > FreebayesSingle (SRR7062654... [ 38%] 282 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fd/ed8429] process > Mpileup (SRR7062654-AADN040... [ 35%] 259 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2493) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [90/adee16] process > FreebayesSingle (SRR7062654... [ 38%] 282 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fd/ed8429] process > Mpileup (SRR7062654-AADN040... [ 35%] 259 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2494) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ba/a34156] process > FreebayesSingle (SRR7062654... [ 38%] 282 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [81/5951dc] process > Mpileup (SRR7062654-AADN040... [ 35%] 260 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2494) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ba/a34156] process > FreebayesSingle (SRR7062654... [ 38%] 282 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [81/5951dc] process > Mpileup (SRR7062654-AADN040... [ 35%] 260 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2496) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9a/577428] process > FreebayesSingle (SRR7062654... [ 39%] 286 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [81/5951dc] process > Mpileup (SRR7062654-AADN040... [ 35%] 260 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2498) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [de/7207b5] process > FreebayesSingle (SRR7062654... [ 39%] 286 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [81/5951dc] process > Mpileup (SRR7062654-AADN040... [ 35%] 260 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2500) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b2/018b04] process > FreebayesSingle (SRR7062654... [ 39%] 290 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [81/5951dc] process > Mpileup (SRR7062654-AADN040... [ 35%] 260 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2502) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [98/93cd73] process > FreebayesSingle (SRR7062654... [ 39%] 290 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [81/5951dc] process > Mpileup (SRR7062654-AADN040... [ 35%] 260 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2503) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [32/527b00] process > FreebayesSingle (SRR7062654... [ 39%] 290 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d3/7d4be7] process > Mpileup (SRR7062654-AADN040... [ 35%] 261 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2506) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [dd/f4cf02] process > FreebayesSingle (SRR7062654... [ 40%] 294 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b8/fe45aa] process > Mpileup (SRR7062654-AADN040... [ 35%] 262 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2508) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [55/fc9516] process > FreebayesSingle (SRR7062654... [ 40%] 294 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b8/fe45aa] process > Mpileup (SRR7062654-AADN040... [ 35%] 262 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2512) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [58/028211] process > FreebayesSingle (SRR7062654... [ 40%] 298 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [5e/f6ff27] process > Mpileup (SRR7062654-AADN040... [ 35%] 262 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2515) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4d/3c52ae] process > FreebayesSingle (SRR7062654... [ 40%] 298 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6a/d4b556] process > Mpileup (SRR7062654-AADN040... [ 36%] 265 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2516) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6e/bffbd4] process > FreebayesSingle (SRR7062654... [ 40%] 298 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/b62a5c] process > Mpileup (SRR7062654-AADN040... [ 36%] 266 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2516) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6e/bffbd4] process > FreebayesSingle (SRR7062654... [ 40%] 298 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/b62a5c] process > Mpileup (SRR7062654-AADN040... [ 36%] 266 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2520) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3f/ec7a65] process > FreebayesSingle (SRR7062654... [ 41%] 302 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6f/6a172c] process > Mpileup (SRR7062654-AADN040... [ 36%] 266 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2525) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a8/9bf1cb] process > FreebayesSingle (SRR7062654... [ 42%] 311 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [68/113a5d] process > Mpileup (SRR7062654-AADN040... [ 36%] 266 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2529) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b9/049963] process > FreebayesSingle (SRR7062654... [ 42%] 311 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [11/0eb90e] process > Mpileup (SRR7062654-AADN040... [ 36%] 266 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2530) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b9/049963] process > FreebayesSingle (SRR7062654... [ 42%] 311 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ed/456c8f] process > Mpileup (SRR7062654-AADN040... [ 36%] 267 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2531) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f4/da001f] process > FreebayesSingle (SRR7062654... [ 42%] 311 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [3f/d0f11c] process > Mpileup (SRR7062654-AADN040... [ 36%] 268 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2531) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f4/da001f] process > FreebayesSingle (SRR7062654... [ 42%] 311 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [de/f7ed95] process > Mpileup (SRR7062654-12_1-19... [ 36%] 269 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2534) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b0/bc1228] process > FreebayesSingle (SRR7062654... [ 42%] 311 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c7/91cc88] process > Mpileup (SRR7062654-AADN040... [ 37%] 271 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2534) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b0/bc1228] process > FreebayesSingle (SRR7062654... [ 42%] 311 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [68/761c02] process > Mpileup (SRR7062654-AADN040... [ 37%] 273 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2536) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b0/bc1228] process > FreebayesSingle (SRR7062654... [ 42%] 311 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/28098b] process > Mpileup (SRR7062654-AADN040... [ 37%] 273 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2537) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f4/da001f] process > FreebayesSingle (SRR7062654... [ 42%] 314 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ac/1d2721] process > Mpileup (SRR7062654-AADN040... [ 37%] 274 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2541) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b0/bc1228] process > FreebayesSingle (SRR7062654... [ 43%] 315 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [78/ade8ba] process > Mpileup (SRR7062654-AADN040... [ 37%] 274 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2542) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b9/049963] process > FreebayesSingle (SRR7062654... [ 43%] 319 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c9/916f51] process > Mpileup (SRR7062654-AADN040... [ 37%] 275 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2546) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [59/fb84fd] process > FreebayesSingle (SRR7062654... [ 43%] 319 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [81/acfa44] process > Mpileup (SRR7062654-AADN040... [ 37%] 275 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2547) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [71/2c2001] process > HaplotypeCaller (SRR7062654... [ 48%] 353 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 353 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [1b/919191] process > FreebayesSingle (SRR7062654... [ 43%] 320 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7d/5ccf25] process > Mpileup (SRR7062654-AADN040... [ 37%] 275 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2548) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [ba/45ee73] process > HaplotypeCaller (SRR7062654... [ 48%] 354 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 354 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [1b/919191] process > FreebayesSingle (SRR7062654... [ 43%] 320 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fe/d25dc7] process > Mpileup (SRR7062654-AADN040... [ 37%] 275 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2550) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [ba/45ee73] process > HaplotypeCaller (SRR7062654... [ 48%] 354 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 354 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9b/0d49c6] process > FreebayesSingle (SRR7062654... [ 43%] 320 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ee/9129bf] process > Mpileup (SRR7062654-AADN040... [ 37%] 277 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2550) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [ba/45ee73] process > HaplotypeCaller (SRR7062654... [ 48%] 354 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 354 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9b/0d49c6] process > FreebayesSingle (SRR7062654... [ 43%] 320 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ee/9129bf] process > Mpileup (SRR7062654-AADN040... [ 37%] 277 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2552) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [16/0f4813] process > FreebayesSingle (SRR7062654... [ 43%] 320 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d5/c1c878] process > Mpileup (SRR7062654-AADN040... [ 38%] 278 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2553) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9b/0d49c6] process > FreebayesSingle (SRR7062654... [ 43%] 321 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c8/4d7f63] process > Mpileup (SRR7062654-KQ75961... [ 38%] 278 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2555) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [c3/5d0857] process > FreebayesSingle (SRR7062654... [ 44%] 323 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1a/164e7d] process > Mpileup (SRR7062654-AADN040... [ 38%] 280 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2557) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f6/a679f8] process > FreebayesSingle (SRR7062654... [ 44%] 323 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f6/d9c248] process > Mpileup (SRR7062654-AADN040... [ 38%] 280 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2558) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [47/9e7352] process > FreebayesSingle (SRR7062654... [ 44%] 323 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [31/c130b4] process > Mpileup (SRR7062654-AADN040... [ 38%] 281 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2560) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [98/fc03a2] process > FreebayesSingle (SRR7062654... [ 44%] 323 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b3/4ee873] process > Mpileup (SRR7062654-AADN040... [ 39%] 285 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2562) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7a/f856c4] process > FreebayesSingle (SRR7062654... [ 44%] 323 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [92/d0d918] process > Mpileup (SRR7062654-AADN040... [ 39%] 285 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2564) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e6/c0af9d] process > FreebayesSingle (SRR7062654... [ 44%] 323 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [67/697e73] process > Mpileup (SRR7062654-AADN040... [ 39%] 287 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2568) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7a/f856c4] process > FreebayesSingle (SRR7062654... [ 44%] 326 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fc/29520b] process > Mpileup (SRR7062654-AADN040... [ 39%] 288 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2572) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2f/25f8c1] process > FreebayesSingle (SRR7062654... [ 44%] 329 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fc/3ca948] process > Mpileup (SRR7062654-AADN040... [ 39%] 290 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2573) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2f/25f8c1] process > FreebayesSingle (SRR7062654... [ 44%] 329 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1c/b634fc] process > Mpileup (SRR7062654-AADN040... [ 39%] 290 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2574) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2c/e9db35] process > FreebayesSingle (SRR7062654... [ 44%] 329 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ae/05a976] process > Mpileup (SRR7062654-AADN040... [ 39%] 291 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2576) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2c/e9db35] process > FreebayesSingle (SRR7062654... [ 44%] 329 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2e/7a01a8] process > Mpileup (SRR7062654-AADN040... [ 40%] 293 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2578) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2f/d8e8f9] process > FreebayesSingle (SRR7062654... [ 44%] 329 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1f/209e31] process > Mpileup (SRR7062654-AADN040... [ 40%] 295 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2578) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2f/d8e8f9] process > FreebayesSingle (SRR7062654... [ 44%] 329 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1f/209e31] process > Mpileup (SRR7062654-AADN040... [ 40%] 295 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2578) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2f/d8e8f9] process > FreebayesSingle (SRR7062654... [ 44%] 329 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1f/209e31] process > Mpileup (SRR7062654-AADN040... [ 40%] 295 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2578) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2f/d8e8f9] process > FreebayesSingle (SRR7062654... [ 44%] 329 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [95/bad891] process > Mpileup (SRR7062654-AADN040... [ 40%] 297 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2581) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7f/aa3945] process > FreebayesSingle (SRR7062654... [ 45%] 330 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [12/e55d5e] process > Mpileup (SRR7062654-AADN040... [ 40%] 297 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2581) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [16/0f4813] process > FreebayesSingle (SRR7062654... [ 45%] 331 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d3/751266] process > Mpileup (SRR7062654-AADN040... [ 40%] 299 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2588) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b5/3b39f8] process > FreebayesSingle (SRR7062654... [ 45%] 335 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d3/751266] process > Mpileup (SRR7062654-AADN040... [ 40%] 299 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2589) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2b/a710a5] process > FreebayesSingle (SRR7062654... [ 45%] 336 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [18/763de4] process > Mpileup (SRR7062654-AADN040... [ 41%] 300 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2590) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [d7/e15e7b] process > FreebayesSingle (SRR7062654... [ 45%] 336 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [18/763de4] process > Mpileup (SRR7062654-AADN040... [ 41%] 300 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2590) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [d7/e15e7b] process > FreebayesSingle (SRR7062654... [ 45%] 336 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cf/7888f3] process > Mpileup (SRR7062654-AADN040... [ 41%] 302 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2592) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [db/a974cd] process > FreebayesSingle (SRR7062654... [ 45%] 336 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cf/7888f3] process > Mpileup (SRR7062654-AADN040... [ 41%] 302 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2593) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2d/ee696c] process > FreebayesSingle (SRR7062654... [ 45%] 336 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9e/b7e2a4] process > Mpileup (SRR7062654-AADN040... [ 41%] 305 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2595) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [18/0844e6] process > FreebayesSingle (SRR7062654... [ 45%] 336 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9e/b7e2a4] process > Mpileup (SRR7062654-AADN040... [ 41%] 305 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2597) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [73/069f4c] process > FreebayesSingle (SRR7062654... [ 46%] 342 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9e/b7e2a4] process > Mpileup (SRR7062654-AADN040... [ 41%] 305 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2601) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [81/af45ca] process > FreebayesSingle (SRR7062654... [ 46%] 342 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9e/b7e2a4] process > Mpileup (SRR7062654-AADN040... [ 41%] 305 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2604) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [fb/0fbb59] process > FreebayesSingle (SRR7062654... [ 47%] 345 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b2/4e47ad] process > Mpileup (SRR7062654-AADN040... [ 41%] 306 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2605) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/1d7fd5] process > FreebayesSingle (SRR7062654... [ 47%] 345 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b2/4e47ad] process > Mpileup (SRR7062654-AADN040... [ 41%] 306 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2607) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9b/c62e81] process > FreebayesSingle (SRR7062654... [ 47%] 347 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b2/4e47ad] process > Mpileup (SRR7062654-AADN040... [ 41%] 306 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2608) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9e/a79884] process > FreebayesSingle (SRR7062654... [ 47%] 348 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b2/4e47ad] process > Mpileup (SRR7062654-AADN040... [ 41%] 306 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2611) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e3/176b9d] process > FreebayesSingle (SRR7062655... [ 47%] 348 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [63/56e66d] process > Mpileup (SRR7062654-AADN040... [ 42%] 309 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2611) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e3/176b9d] process > FreebayesSingle (SRR7062655... [ 47%] 348 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [63/56e66d] process > Mpileup (SRR7062654-AADN040... [ 42%] 309 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2615) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [25/1bbd8c] process > FreebayesSingle (SRR7062655... [ 48%] 354 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8f/c9392f] process > Mpileup (SRR7062655-12_1-19... [ 42%] 309 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2617) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [af/fe955c] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ea/0a97c5] process > FreebayesSingle (SRR7062655... [ 48%] 354 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8f/c9392f] process > Mpileup (SRR7062655-12_1-19... [ 42%] 309 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2621) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [bc/985748] process > FreebayesSingle (SRR7062655... [ 49%] 363 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [bf/a37819] process > Mpileup (SRR7062654-AADN040... [ 42%] 311 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2626) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [d6/8f5d4c] process > FreebayesSingle (SRR7062655... [ 49%] 363 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [bf/a37819] process > Mpileup (SRR7062654-AADN040... [ 42%] 311 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2628) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [cd/3e59a4] process > FreebayesSingle (SRR7062655... [ 49%] 363 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [bf/a37819] process > Mpileup (SRR7062654-AADN040... [ 42%] 311 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2629) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [91/2c8da9] process > FreebayesSingle (SRR7062654... [ 50%] 368 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/df3856] process > Mpileup (SRR7062654-AADN040... [ 42%] 312 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2634) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [91/2c8da9] process > FreebayesSingle (SRR7062654... [ 50%] 368 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6d/4a2b46] process > Mpileup (SRR7062655-Z_1-823... [ 42%] 312 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2635) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [91/2c8da9] process > FreebayesSingle (SRR7062654... [ 50%] 368 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8b/d53b94] process > Mpileup (SRR7062655-2_1-149... [ 43%] 316 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2638) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3f/6d68f6] process > FreebayesSingle (SRR7062655... [ 50%] 368 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8b/d53b94] process > Mpileup (SRR7062655-2_1-149... [ 43%] 316 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2639) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3f/6d68f6] process > FreebayesSingle (SRR7062655... [ 50%] 368 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [80/a68a45] process > Mpileup (SRR7062655-19_1-99... [ 43%] 317 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2639) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3f/6d68f6] process > FreebayesSingle (SRR7062655... [ 50%] 368 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [80/a68a45] process > Mpileup (SRR7062655-19_1-99... [ 43%] 317 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2640) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3f/6d68f6] process > FreebayesSingle (SRR7062655... [ 50%] 369 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a9/4378de] process > Mpileup (SRR7062655-17_1-10... [ 43%] 317 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2641) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f0/f26689] process > FreebayesSingle (SRR7062655... [ 50%] 373 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [ 43%] 317 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2644) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [09/cc4502] process > FreebayesSingle (SRR7062655... [ 50%] 373 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [ 43%] 317 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2647) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [17/62f693] process > FreebayesSingle (SRR7062655... [ 51%] 375 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [5b/0d2089] process > Mpileup (SRR7062654-AADN040... [ 43%] 318 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2650) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b2/032318] process > FreebayesSingle (SRR7062655... [ 51%] 378 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [5b/0d2089] process > Mpileup (SRR7062654-AADN040... [ 43%] 318 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2651) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [1c/ac4984] process > FreebayesSingle (SRR7062655... [ 51%] 378 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6f/da1452] process > Mpileup (SRR7062654-AADN040... [ 43%] 319 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2651) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [1c/ac4984] process > FreebayesSingle (SRR7062655... [ 51%] 378 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6f/da1452] process > Mpileup (SRR7062654-AADN040... [ 43%] 319 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2652) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5e/661724] process > FreebayesSingle (SRR7062655... [ 51%] 379 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6f/da1452] process > Mpileup (SRR7062654-AADN040... [ 43%] 319 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2655) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [38/e03ef8] process > FreebayesSingle (SRR7062655... [ 52%] 382 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6f/da1452] process > Mpileup (SRR7062654-AADN040... [ 43%] 319 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2656) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [12/19aab7] process > FreebayesSingle (SRR7062655... [ 52%] 383 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6f/da1452] process > Mpileup (SRR7062654-AADN040... [ 43%] 319 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2659) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [68/9b38bf] process > FreebayesSingle (SRR7062655... [ 52%] 385 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [aa/718329] process > Mpileup (SRR7062654-8_1-299... [ 43%] 320 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2659) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [68/9b38bf] process > FreebayesSingle (SRR7062655... [ 52%] 385 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [aa/718329] process > Mpileup (SRR7062654-8_1-299... [ 43%] 320 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2662) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [c6/a9b9ff] process > FreebayesSingle (SRR7062655... [ 52%] 388 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/f9eadf] process > Mpileup (SRR7062655-11_1-20... [ 43%] 320 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2663) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a6/89b358] process > FreebayesSingle (SRR7062655... [ 53%] 389 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1b/fd27ff] process > Mpileup (SRR7062655-15_1-12... [ 43%] 320 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2663) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b0/abc110] process > FreebayesSingle (SRR7062655... [ 53%] 390 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1b/fd27ff] process > Mpileup (SRR7062655-15_1-12... [ 43%] 320 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2664) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b0/abc110] process > FreebayesSingle (SRR7062655... [ 53%] 390 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c6/836c22] process > Mpileup (SRR7062655-9_1-240... [ 43%] 320 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2664) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b0/abc110] process > FreebayesSingle (SRR7062655... [ 53%] 390 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/2d9dc7] process > Mpileup (SRR7062654-AADN040... [ 44%] 323 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2668) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4d/2c60c4] process > FreebayesSingle (SRR7062655... [ 53%] 390 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f9/ec076d] process > Mpileup (SRR7062655-8_1-299... [ 44%] 324 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2668) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4d/2c60c4] process > FreebayesSingle (SRR7062655... [ 53%] 390 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c0/3caf06] process > Mpileup (SRR7062654-AADN040... [ 44%] 325 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2669) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [47/de8064] process > FreebayesSingle (SRR7062655... [ 53%] 390 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c0/3caf06] process > Mpileup (SRR7062654-AADN040... [ 44%] 325 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2670) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4a/9678c0] process > FreebayesSingle (SRR7062655... [ 53%] 391 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c0/3caf06] process > Mpileup (SRR7062654-AADN040... [ 44%] 325 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2671) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0c/5e83ab] process > FreebayesSingle (SRR7062655... [ 53%] 392 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c0/3caf06] process > Mpileup (SRR7062654-AADN040... [ 44%] 325 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2672) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [d4/58b19c] process > FreebayesSingle (SRR7062655... [ 53%] 392 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [90/08f0a7] process > Mpileup (SRR7062654-AADN040... [ 44%] 326 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2674) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [25/6a710f] process > FreebayesSingle (SRR7062655... [ 53%] 392 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/10b0dd] process > Mpileup (SRR7062654-AADN040... [ 45%] 330 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2676) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [df/c4456d] process > FreebayesSingle (SRR7062655... [ 53%] 392 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/10b0dd] process > Mpileup (SRR7062654-AADN040... [ 45%] 330 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2676) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [df/c4456d] process > FreebayesSingle (SRR7062655... [ 53%] 392 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/10b0dd] process > Mpileup (SRR7062654-AADN040... [ 45%] 330 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2678) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b7/8e3b0c] process > FreebayesSingle (SRR7062655... [ 53%] 393 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c7/91cc88] process > Mpileup (SRR7062654-AADN040... [ 45%] 331 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2681) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [1d/6721a0] process > HaplotypeCaller (SRR7062654... [ 48%] 355 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 355 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [ 53%] 395 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [5d/aa4678] process > Mpileup (SRR7062654-AADN040... [ 45%] 332 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2684) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [39/e66f92] process > HaplotypeCaller (SRR7062654... [ 48%] 356 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 356 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [1c/c44265] process > FreebayesSingle (SRR7062655... [ 54%] 396 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [42/5e7b39] process > Mpileup (SRR7062654-6_1-354... [ 45%] 333 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2685) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [39/e66f92] process > HaplotypeCaller (SRR7062654... [ 48%] 356 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 356 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/7f3f6a] process > FreebayesSingle (SRR7062655... [ 54%] 398 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d5/c1c878] process > Mpileup (SRR7062654-AADN040... [ 45%] 334 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2687) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [b2/65b1bb] process > HaplotypeCaller (SRR7062655... [ 48%] 356 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 356 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/7f3f6a] process > FreebayesSingle (SRR7062655... [ 54%] 398 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d5/c1c878] process > Mpileup (SRR7062654-AADN040... [ 45%] 334 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2690) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [04/54036b] process > HaplotypeCaller (SRR7062655... [ 48%] 356 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 356 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/7f3f6a] process > FreebayesSingle (SRR7062655... [ 54%] 398 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f6/d9c248] process > Mpileup (SRR7062654-AADN040... [ 46%] 337 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2691) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [e7/00fdb1] process > HaplotypeCaller (SRR7062655... [ 48%] 356 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 356 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [d8/fbac68] process > FreebayesSingle (SRR7062655... [ 54%] 399 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f6/d9c248] process > Mpileup (SRR7062654-AADN040... [ 46%] 337 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2692) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [21/d74423] process > BamQC (F_Aln-SNP-SRR7062654) [ 75%] 3 of 4 [e7/00fdb1] process > HaplotypeCaller (SRR7062655... [ 48%] 356 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 356 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/7f3f6a] process > FreebayesSingle (SRR7062655... [ 54%] 400 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cc/f54be7] process > Mpileup (SRR7062655-18_1-11... [ 46%] 337 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2696) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [bf/02716b] process > HaplotypeCaller (SRR7062655... [ 48%] 356 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 356 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [ 54%] 403 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [92/d0d918] process > Mpileup (SRR7062654-AADN040... [ 46%] 338 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2698) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [72/27a161] process > HaplotypeCaller (SRR7062655... [ 48%] 356 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 356 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6a/053794] process > FreebayesSingle (SRR7062655... [ 55%] 404 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2e/7a01a8] process > Mpileup (SRR7062654-AADN040... [ 46%] 339 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2703) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [0a/bb8316] process > HaplotypeCaller (SRR7062655... [ 48%] 356 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 356 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a5/db0e68] process > FreebayesSingle (SRR7062655... [ 55%] 406 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [25/66f980] process > Mpileup (SRR7062655-3_1-111... [ 46%] 342 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2703) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [0a/bb8316] process > HaplotypeCaller (SRR7062655... [ 48%] 356 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 356 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a5/db0e68] process > FreebayesSingle (SRR7062655... [ 55%] 406 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [25/66f980] process > Mpileup (SRR7062655-3_1-111... [ 46%] 342 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2703) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [0a/bb8316] process > HaplotypeCaller (SRR7062655... [ 48%] 356 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 356 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a5/db0e68] process > FreebayesSingle (SRR7062655... [ 55%] 406 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [25/66f980] process > Mpileup (SRR7062655-3_1-111... [ 46%] 342 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2703) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [ac/88c975] process > HaplotypeCaller (SRR7062655... [ 48%] 357 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 356 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [d0/bd4d3f] process > FreebayesSingle (SRR7062655... [ 55%] 407 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [25/66f980] process > Mpileup (SRR7062655-3_1-111... [ 46%] 342 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2705) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [1b/e71eae] process > HaplotypeCaller (SRR7062655... [ 48%] 358 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 358 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [62/e4436a] process > FreebayesSingle (SRR7062655... [ 55%] 407 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [25/66f980] process > Mpileup (SRR7062655-3_1-111... [ 46%] 342 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2706) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [f7/83aaf7] process > HaplotypeCaller (SRR7062655... [ 48%] 358 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 358 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [62/e4436a] process > FreebayesSingle (SRR7062655... [ 55%] 407 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [25/66f980] process > Mpileup (SRR7062655-3_1-111... [ 46%] 342 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2707) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [b2/65b1bb] process > HaplotypeCaller (SRR7062655... [ 49%] 359 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 359 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a5/2d5246] process > FreebayesSingle (SRR7062655... [ 55%] 407 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [25/66f980] process > Mpileup (SRR7062655-3_1-111... [ 46%] 342 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2708) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [7b/4ab7ba] process > HaplotypeCaller (SRR7062654... [ 49%] 360 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 360 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [ 55%] 407 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b3/4ee873] process > Mpileup (SRR7062654-AADN040... [ 46%] 343 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2709) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [4f/70ac3f] process > HaplotypeCaller (SRR7062655... [ 49%] 360 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 360 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [ 55%] 407 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b3/4ee873] process > Mpileup (SRR7062654-AADN040... [ 46%] 343 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2709) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [bb/352af5] process > HaplotypeCaller (SRR7062655... [ 49%] 361 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 361 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [ 55%] 407 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b3/4ee873] process > Mpileup (SRR7062654-AADN040... [ 46%] 343 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2710) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [f4/a27240] process > HaplotypeCaller (SRR7062655... [ 49%] 361 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 361 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [ 55%] 407 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b3/4ee873] process > Mpileup (SRR7062654-AADN040... [ 46%] 343 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2712) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 49%] 362 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 362 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [62/e4436a] process > FreebayesSingle (SRR7062655... [ 55%] 408 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b3/4ee873] process > Mpileup (SRR7062654-AADN040... [ 46%] 343 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2714) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [b8/aee8d9] process > HaplotypeCaller (SRR7062655... [ 49%] 362 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 362 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [fb/4cdef3] process > FreebayesSingle (SRR7062655... [ 55%] 410 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b3/4ee873] process > Mpileup (SRR7062654-AADN040... [ 46%] 343 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2716) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [a3/da0b70] process > HaplotypeCaller (SRR7062655... [ 49%] 362 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 362 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [fb/4cdef3] process > FreebayesSingle (SRR7062655... [ 55%] 410 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [33/531201] process > Mpileup (SRR7062654-AADN040... [ 47%] 345 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2719) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [f6/d3cd48] process > HaplotypeCaller (SRR7062655... [ 49%] 362 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 362 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [fb/4cdef3] process > FreebayesSingle (SRR7062655... [ 55%] 410 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fe/d25dc7] process > Mpileup (SRR7062654-AADN040... [ 47%] 348 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2719) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [f6/d3cd48] process > HaplotypeCaller (SRR7062655... [ 49%] 362 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 362 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [fb/4cdef3] process > FreebayesSingle (SRR7062655... [ 55%] 410 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fe/d25dc7] process > Mpileup (SRR7062654-AADN040... [ 47%] 348 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2722) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [52/fd43fc] process > HaplotypeCaller (SRR7062655... [ 49%] 363 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 363 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [89/63005a] process > FreebayesSingle (SRR7062655... [ 56%] 411 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [81/acfa44] process > Mpileup (SRR7062654-AADN040... [ 47%] 350 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2723) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8a/f5282d] process > HaplotypeCaller (SRR7062655... [ 49%] 363 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 363 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [89/63005a] process > FreebayesSingle (SRR7062655... [ 56%] 411 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [81/acfa44] process > Mpileup (SRR7062654-AADN040... [ 47%] 350 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2724) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [d3/477598] process > HaplotypeCaller (SRR7062655... [ 49%] 363 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 363 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [c8/f38e32] process > FreebayesSingle (SRR7062655... [ 56%] 412 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [81/acfa44] process > Mpileup (SRR7062654-AADN040... [ 47%] 350 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2725) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [66/e829a2] process > HaplotypeCaller (SRR7062655... [ 49%] 363 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 363 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [04/d444da] process > FreebayesSingle (SRR7062654... [ 56%] 413 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [81/acfa44] process > Mpileup (SRR7062654-AADN040... [ 47%] 350 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2727) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [a2/3c98a4] process > HaplotypeCaller (SRR7062655... [ 49%] 364 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 364 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [04/d444da] process > FreebayesSingle (SRR7062654... [ 56%] 413 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ed/456c8f] process > Mpileup (SRR7062654-AADN040... [ 47%] 351 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2728) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [a2/3c98a4] process > HaplotypeCaller (SRR7062655... [ 49%] 364 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 364 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f7/db47b2] process > FreebayesSingle (SRR7062655... [ 56%] 413 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d9/a6f184] process > Mpileup (SRR7062654-AADN040... [ 48%] 352 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2729) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [06/cdb810] process > HaplotypeCaller (SRR7062655... [ 49%] 365 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 365 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4d/19aff0] process > FreebayesSingle (SRR7062655... [ 56%] 413 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d9/a6f184] process > Mpileup (SRR7062654-AADN040... [ 48%] 352 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2730) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [06/cdb810] process > HaplotypeCaller (SRR7062655... [ 49%] 365 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 365 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [c6/55a739] process > FreebayesSingle (SRR7062655... [ 56%] 414 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d9/a6f184] process > Mpileup (SRR7062654-AADN040... [ 48%] 352 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2732) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [f4/a27240] process > HaplotypeCaller (SRR7062655... [ 49%] 366 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 366 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [96/fa29c8] process > FreebayesSingle (SRR7062655... [ 56%] 414 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [60/e26c29] process > Mpileup (SRR7062654-AADN040... [ 48%] 353 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2734) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [f4/a27240] process > HaplotypeCaller (SRR7062655... [ 49%] 366 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 366 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a8/23066b] process > FreebayesSingle (SRR7062655... [ 56%] 415 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2d/79199c] process > Mpileup (SRR7062654-7_1-369... [ 48%] 354 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2735) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [97/b5452c] process > HaplotypeCaller (SRR7062655... [ 49%] 366 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 366 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [25/6a710f] process > FreebayesSingle (SRR7062655... [ 56%] 416 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2d/79199c] process > Mpileup (SRR7062654-7_1-369... [ 48%] 354 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2738) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 50%] 367 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 367 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [09/cc4502] process > FreebayesSingle (SRR7062655... [ 56%] 417 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1c/b634fc] process > Mpileup (SRR7062654-AADN040... [ 48%] 355 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2738) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 50%] 367 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 367 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [09/cc4502] process > FreebayesSingle (SRR7062655... [ 56%] 417 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8a/180f66] process > Mpileup (SRR7062654-AADN040... [ 48%] 356 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2741) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [e5/a96080] process > HaplotypeCaller (SRR7062655... [ 50%] 369 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 369 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [09/cc4502] process > FreebayesSingle (SRR7062655... [ 56%] 417 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8a/180f66] process > Mpileup (SRR7062654-AADN040... [ 48%] 356 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2742) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [f6/7c2a49] process > HaplotypeCaller (SRR7062655... [ 50%] 371 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 371 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e6/0d079b] process > FreebayesSingle (SRR7062655... [ 56%] 418 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8a/180f66] process > Mpileup (SRR7062654-AADN040... [ 48%] 356 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2744) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [28/fe54f7] process > HaplotypeCaller (SRR7062655... [ 50%] 371 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 371 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e6/0d079b] process > FreebayesSingle (SRR7062655... [ 56%] 418 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8a/180f66] process > Mpileup (SRR7062654-AADN040... [ 48%] 356 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2745) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [1d/ac2c81] process > HaplotypeCaller (SRR7062655... [ 50%] 371 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 371 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a8/23066b] process > FreebayesSingle (SRR7062655... [ 57%] 421 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f0/edb19b] process > Mpileup (SRR7062654-AADN040... [ 48%] 357 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2748) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [2a/ebb3a7] process > HaplotypeCaller (SRR7062655... [ 50%] 371 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 371 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a8/23066b] process > FreebayesSingle (SRR7062655... [ 57%] 421 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f0/edb19b] process > Mpileup (SRR7062654-AADN040... [ 48%] 357 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2751) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [7d/da4654] process > HaplotypeCaller (SRR7062655... [ 50%] 373 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 373 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [96/fa29c8] process > FreebayesSingle (SRR7062655... [ 57%] 423 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f0/edb19b] process > Mpileup (SRR7062654-AADN040... [ 48%] 357 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2752) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [49/e38384] process > HaplotypeCaller (SRR7062655... [ 50%] 373 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 373 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [96/fa29c8] process > FreebayesSingle (SRR7062655... [ 57%] 423 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f0/edb19b] process > Mpileup (SRR7062654-AADN040... [ 48%] 357 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2754) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [2c/1c1617] process > HaplotypeCaller (SRR7062655... [ 51%] 374 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 374 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [96/fa29c8] process > FreebayesSingle (SRR7062655... [ 57%] 423 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fc/29520b] process > Mpileup (SRR7062654-AADN040... [ 49%] 359 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2755) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [93/de8ab8] process > HaplotypeCaller (SRR7062655... [ 51%] 374 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 374 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [96/fa29c8] process > FreebayesSingle (SRR7062655... [ 57%] 423 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fc/29520b] process > Mpileup (SRR7062654-AADN040... [ 49%] 359 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2755) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [93/de8ab8] process > HaplotypeCaller (SRR7062655... [ 51%] 374 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 374 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [96/fa29c8] process > FreebayesSingle (SRR7062655... [ 57%] 423 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fc/29520b] process > Mpileup (SRR7062654-AADN040... [ 49%] 359 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2757) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [47/7da5c7] process > HaplotypeCaller (SRR7062655... [ 51%] 375 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 375 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [96/fa29c8] process > FreebayesSingle (SRR7062655... [ 57%] 423 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [78/ade8ba] process > Mpileup (SRR7062654-AADN040... [ 49%] 360 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2759) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [ae/fc8d69] process > HaplotypeCaller (SRR7062655... [ 51%] 377 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 377 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [96/fa29c8] process > FreebayesSingle (SRR7062655... [ 57%] 423 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [78/ade8ba] process > Mpileup (SRR7062654-AADN040... [ 49%] 360 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2761) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [c0/25e6db] process > HaplotypeCaller (SRR7062655... [ 51%] 378 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 378 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [d9/f0d3fc] process > FreebayesSingle (SRR7062655... [ 57%] 424 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [78/ade8ba] process > Mpileup (SRR7062654-AADN040... [ 49%] 360 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2762) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [1e/44f518] process > HaplotypeCaller (SRR7062655... [ 51%] 379 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 379 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [d9/f0d3fc] process > FreebayesSingle (SRR7062655... [ 57%] 424 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [78/ade8ba] process > Mpileup (SRR7062654-AADN040... [ 49%] 360 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2764) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [0d/5a71bd] process > HaplotypeCaller (SRR7062655... [ 51%] 379 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 379 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3b/8efd8d] process > FreebayesSingle (SRR7062655... [ 57%] 425 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a5/48c571] process > Mpileup (SRR7062654-AADN040... [ 49%] 361 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2766) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [49/e38384] process > HaplotypeCaller (SRR7062655... [ 51%] 381 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 381 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [af/251d4f] process > FreebayesSingle (SRR7062655... [ 57%] 425 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a5/48c571] process > Mpileup (SRR7062654-AADN040... [ 49%] 361 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2768) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [2a/ebb3a7] process > HaplotypeCaller (SRR7062655... [ 52%] 383 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 383 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [73/8cfe01] process > FreebayesSingle (SRR7062655... [ 57%] 425 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a5/48c571] process > Mpileup (SRR7062654-AADN040... [ 49%] 361 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2770) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [43/8201c9] process > HaplotypeCaller (SRR7062655... [ 52%] 384 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 384 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [df/24607c] process > FreebayesSingle (SRR7062655... [ 57%] 425 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [12/e55d5e] process > Mpileup (SRR7062654-AADN040... [ 49%] 362 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2770) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [43/8201c9] process > HaplotypeCaller (SRR7062655... [ 52%] 384 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 384 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [df/24607c] process > FreebayesSingle (SRR7062655... [ 57%] 425 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [26/9757ff] process > Mpileup (SRR7062654-AADN040... [ 49%] 363 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2771) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [43/8201c9] process > HaplotypeCaller (SRR7062655... [ 52%] 384 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 384 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [74/b94b1c] process > FreebayesSingle (SRR7062655... [ 57%] 425 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [26/9757ff] process > Mpileup (SRR7062654-AADN040... [ 49%] 363 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2771) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [43/8201c9] process > HaplotypeCaller (SRR7062655... [ 52%] 384 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 384 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [74/b94b1c] process > FreebayesSingle (SRR7062655... [ 57%] 425 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [26/9757ff] process > Mpileup (SRR7062654-AADN040... [ 49%] 363 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2771) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [43/8201c9] process > HaplotypeCaller (SRR7062655... [ 52%] 384 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 384 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [74/b94b1c] process > FreebayesSingle (SRR7062655... [ 57%] 425 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [26/9757ff] process > Mpileup (SRR7062654-AADN040... [ 49%] 363 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2772) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [43/8201c9] process > HaplotypeCaller (SRR7062655... [ 52%] 384 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 384 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a0/596009] process > FreebayesSingle (SRR7062655... [ 58%] 426 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [26/9757ff] process > Mpileup (SRR7062654-AADN040... [ 49%] 363 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2773) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [a0/bfbde3] process > HaplotypeCaller (SRR7062655... [ 52%] 384 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 384 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [df/24607c] process > FreebayesSingle (SRR7062655... [ 58%] 431 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [26/9757ff] process > Mpileup (SRR7062654-AADN040... [ 49%] 363 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2777) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [38/fad283] process > HaplotypeCaller (SRR7062655... [ 52%] 384 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 384 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [27/06f85c] process > FreebayesSingle (SRR7062655... [ 58%] 431 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [26/9757ff] process > Mpileup (SRR7062654-AADN040... [ 49%] 363 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2778) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [b7/4434c3] process > HaplotypeCaller (SRR7062655... [ 52%] 387 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 387 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e0/987860] process > FreebayesSingle (SRR7062655... [ 58%] 432 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [94/c62787] process > Mpileup (SRR7062654-AADN040... [ 49%] 365 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2783) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [6a/73d107] process > HaplotypeCaller (SRR7062655... [ 52%] 387 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 387 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [81/9cb7ef] process > FreebayesSingle (SRR7062655... [ 58%] 432 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [94/c62787] process > Mpileup (SRR7062654-AADN040... [ 49%] 365 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2784) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [00/50bf4a] process > HaplotypeCaller (SRR7062655... [ 52%] 388 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 388 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f7/788353] process > FreebayesSingle (SRR7062655... [ 59%] 433 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [94/c62787] process > Mpileup (SRR7062654-AADN040... [ 49%] 365 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2785) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [00/50bf4a] process > HaplotypeCaller (SRR7062655... [ 52%] 388 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 388 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6d/f9a415] process > FreebayesSingle (SRR7062655... [ 59%] 433 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [94/c62787] process > Mpileup (SRR7062654-AADN040... [ 49%] 365 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2787) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [1e/44f518] process > HaplotypeCaller (SRR7062655... [ 53%] 389 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 389 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e1/98c189] process > FreebayesSingle (SRR7062655... [ 59%] 435 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [94/c62787] process > Mpileup (SRR7062654-AADN040... [ 49%] 365 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2788) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [be/0cac76] process > HaplotypeCaller (SRR7062655... [ 53%] 389 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 389 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e1/98c189] process > FreebayesSingle (SRR7062655... [ 59%] 435 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [94/c62787] process > Mpileup (SRR7062654-AADN040... [ 49%] 365 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2791) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [be/0cac76] process > HaplotypeCaller (SRR7062655... [ 53%] 389 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 389 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [8a/e887cf] process > FreebayesSingle (SRR7062655... [ 59%] 438 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [94/c62787] process > Mpileup (SRR7062654-AADN040... [ 49%] 365 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2794) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [46/94aa4d] process > HaplotypeCaller (SRR7062655... [ 53%] 390 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 390 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [85/2103ab] process > FreebayesSingle (SRR7062655... [ 59%] 439 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fc/3ca948] process > Mpileup (SRR7062654-AADN040... [ 49%] 366 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2795) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [42/29bc54] process > HaplotypeCaller (SRR7062655... [ 53%] 391 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 391 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [bb/624dd3] process > FreebayesSingle (SRR7062655... [ 59%] 439 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fc/3ca948] process > Mpileup (SRR7062654-AADN040... [ 49%] 366 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2796) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [b7/219434] process > HaplotypeCaller (SRR7062655... [ 53%] 392 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 392 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [14/e84eb3] process > FreebayesSingle (SRR7062655... [ 59%] 439 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fc/3ca948] process > Mpileup (SRR7062654-AADN040... [ 49%] 366 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2800) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [db/b1055f] process > HaplotypeCaller (SRR7062655... [ 53%] 394 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 394 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/6f5b3d] process > FreebayesSingle (SRR7062655... [ 60%] 444 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fc/3ca948] process > Mpileup (SRR7062654-AADN040... [ 49%] 366 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2803) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [b7/388111] process > HaplotypeCaller (SRR7062655... [ 53%] 394 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 394 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/3e9505] process > FreebayesSingle (SRR7062655... [ 60%] 444 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fc/3ca948] process > Mpileup (SRR7062654-AADN040... [ 49%] 366 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2808) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [4f/14a99b] process > HaplotypeCaller (SRR7062655... [ 53%] 395 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 395 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [25/032141] process > FreebayesSingle (SRR7062655... [ 61%] 448 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fc/3ca948] process > Mpileup (SRR7062654-AADN040... [ 49%] 366 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2809) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [97/7596d9] process > HaplotypeCaller (SRR7062655... [ 54%] 396 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 396 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [c8/8a18a4] process > FreebayesSingle (SRR7062655... [ 61%] 448 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fc/3ca948] process > Mpileup (SRR7062654-AADN040... [ 49%] 366 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2809) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [97/7596d9] process > HaplotypeCaller (SRR7062655... [ 54%] 396 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 396 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [c8/8a18a4] process > FreebayesSingle (SRR7062655... [ 61%] 448 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c4/9531c7] process > Mpileup (SRR7062654-1_1-196... [ 50%] 367 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2810) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [97/7596d9] process > HaplotypeCaller (SRR7062655... [ 54%] 396 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 396 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [94/c37678] process > FreebayesSingle (SRR7062655... [ 61%] 448 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c4/9531c7] process > Mpileup (SRR7062654-1_1-196... [ 50%] 367 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2810) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [46/94aa4d] process > HaplotypeCaller (SRR7062655... [ 54%] 397 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 397 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [65/016bd9] process > FreebayesSingle (SRR7062655... [ 61%] 449 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c4/9531c7] process > Mpileup (SRR7062654-1_1-196... [ 50%] 367 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2813) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [46/94aa4d] process > HaplotypeCaller (SRR7062655... [ 54%] 397 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 397 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/631adf] process > FreebayesSingle (SRR7062655... [ 61%] 450 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c4/9531c7] process > Mpileup (SRR7062654-1_1-196... [ 50%] 367 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2814) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [be/0cac76] process > HaplotypeCaller (SRR7062655... [ 54%] 399 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 399 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4f/7125c3] process > FreebayesSingle (SRR7062655... [ 61%] 453 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c4/9531c7] process > Mpileup (SRR7062654-1_1-196... [ 50%] 367 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2819) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [be/0cac76] process > HaplotypeCaller (SRR7062655... [ 54%] 399 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 399 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9a/ee66e0] process > FreebayesSingle (SRR7062655... [ 62%] 459 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c4/9531c7] process > Mpileup (SRR7062654-1_1-196... [ 50%] 367 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2824) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [0b/73decd] process > HaplotypeCaller (SRR7062655... [ 54%] 399 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 399 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [00/9e43b5] process > FreebayesSingle (SRR7062655... [ 62%] 459 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c4/9531c7] process > Mpileup (SRR7062654-1_1-196... [ 50%] 367 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2825) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [59/079aed] process > HaplotypeCaller (SRR7062655... [ 54%] 399 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 399 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [94/c37678] process > FreebayesSingle (SRR7062655... [ 62%] 462 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [4a/571cb8] process > Mpileup (SRR7062655-14_1-15... [ 50%] 368 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2828) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [59/079aed] process > HaplotypeCaller (SRR7062655... [ 54%] 399 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 399 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3f/884bd7] process > FreebayesSingle (SRR7062655... [ 62%] 462 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [4a/571cb8] process > Mpileup (SRR7062655-14_1-15... [ 50%] 368 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2830) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [db/b1055f] process > HaplotypeCaller (SRR7062655... [ 54%] 401 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 401 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/2aca9d] process > FreebayesSingle (SRR7062655... [ 62%] 462 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [4a/571cb8] process > Mpileup (SRR7062655-14_1-15... [ 50%] 368 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2832) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [5b/8825af] process > HaplotypeCaller (SRR7062655... [ 54%] 402 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 402 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0b/78976b] process > FreebayesSingle (SRR7062655... [ 63%] 464 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [4a/571cb8] process > Mpileup (SRR7062655-14_1-15... [ 50%] 368 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2835) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [5b/8825af] process > HaplotypeCaller (SRR7062655... [ 54%] 402 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 402 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [c2/9e229b] process > FreebayesSingle (SRR7062655... [ 63%] 466 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [4a/571cb8] process > Mpileup (SRR7062655-14_1-15... [ 50%] 368 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2837) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [f0/4ba572] process > HaplotypeCaller (SRR7062655... [ 54%] 403 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 403 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [99/101f41] process > FreebayesSingle (SRR7062655... [ 64%] 473 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [4a/571cb8] process > Mpileup (SRR7062655-14_1-15... [ 50%] 368 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2842) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [81/a607f0] process > HaplotypeCaller (SRR7062655... [ 54%] 403 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 403 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0d/3a8ca1] process > FreebayesSingle (SRR7062655... [ 64%] 473 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [4a/571cb8] process > Mpileup (SRR7062655-14_1-15... [ 50%] 368 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2843) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [c7/35477e] process > HaplotypeCaller (SRR7062655... [ 54%] 403 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 403 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0d/3a8ca1] process > FreebayesSingle (SRR7062655... [ 64%] 473 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [4a/571cb8] process > Mpileup (SRR7062655-14_1-15... [ 50%] 368 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2847) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [16/73ce00] process > HaplotypeCaller (SRR7062655... [ 55%] 404 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 404 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [55/a3ccef] process > FreebayesSingle (SRR7062655... [ 65%] 480 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [4a/571cb8] process > Mpileup (SRR7062655-14_1-15... [ 50%] 368 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2851) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [b3/a35325] process > HaplotypeCaller (SRR7062655... [ 55%] 404 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 404 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [55/a3ccef] process > FreebayesSingle (SRR7062655... [ 65%] 480 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [4a/571cb8] process > Mpileup (SRR7062655-14_1-15... [ 50%] 368 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2852) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [4d/de3b9a] process > HaplotypeCaller (SRR7062655... [ 55%] 405 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 405 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [55/a3ccef] process > FreebayesSingle (SRR7062655... [ 65%] 480 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [4a/571cb8] process > Mpileup (SRR7062655-14_1-15... [ 50%] 368 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2856) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [30/85c99d] process > HaplotypeCaller (SRR7062655... [ 55%] 405 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 405 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [53/05ed46] process > FreebayesSingle (SRR7062655... [ 65%] 483 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [30/47286b] process > Mpileup (SRR7062655-13_1-18... [ 50%] 369 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2856) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [30/85c99d] process > HaplotypeCaller (SRR7062655... [ 55%] 405 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 405 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [c2/9e229b] process > FreebayesSingle (SRR7062655... [ 65%] 484 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [30/47286b] process > Mpileup (SRR7062655-13_1-18... [ 50%] 369 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2860) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [a8/0d0c42] process > HaplotypeCaller (SRR7062655... [ 55%] 405 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 405 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [55/a3ccef] process > FreebayesSingle (SRR7062655... [ 66%] 487 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [30/47286b] process > Mpileup (SRR7062655-13_1-18... [ 50%] 369 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2860) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [a8/0d0c42] process > HaplotypeCaller (SRR7062655... [ 55%] 405 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 405 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b7/8e3b0c] process > FreebayesSingle (SRR7062655... [ 66%] 488 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [30/47286b] process > Mpileup (SRR7062655-13_1-18... [ 50%] 369 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2861) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [82/d3b986] process > HaplotypeCaller (SRR7062655... [ 55%] 405 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 405 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b7/8e3b0c] process > FreebayesSingle (SRR7062655... [ 66%] 488 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [30/47286b] process > Mpileup (SRR7062655-13_1-18... [ 50%] 369 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2862) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [66/8630d6] process > HaplotypeCaller (SRR7062655... [ 55%] 407 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 407 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b7/8e3b0c] process > FreebayesSingle (SRR7062655... [ 66%] 488 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [30/47286b] process > Mpileup (SRR7062655-13_1-18... [ 50%] 369 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2863) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [24/d7f387] process > HaplotypeCaller (SRR7062655... [ 55%] 407 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 407 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b7/8e3b0c] process > FreebayesSingle (SRR7062655... [ 66%] 488 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [30/47286b] process > Mpileup (SRR7062655-13_1-18... [ 50%] 369 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2864) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [4e/bb9cac] process > HaplotypeCaller (SRR7062655... [ 56%] 411 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 411 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b7/8e3b0c] process > FreebayesSingle (SRR7062655... [ 66%] 488 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [30/47286b] process > Mpileup (SRR7062655-13_1-18... [ 50%] 369 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2867) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [9e/3a058b] process > HaplotypeCaller (SRR7062655... [ 56%] 411 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 411 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b7/8e3b0c] process > FreebayesSingle (SRR7062655... [ 66%] 488 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [30/47286b] process > Mpileup (SRR7062655-13_1-18... [ 50%] 369 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2869) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [1d/d3fc81] process > HaplotypeCaller (SRR7062655... [ 56%] 414 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 414 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b7/8e3b0c] process > FreebayesSingle (SRR7062655... [ 66%] 488 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [30/47286b] process > Mpileup (SRR7062655-13_1-18... [ 50%] 369 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2870) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [4d/7f0a2c] process > HaplotypeCaller (SRR7062655... [ 56%] 414 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 414 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b7/8e3b0c] process > FreebayesSingle (SRR7062655... [ 66%] 488 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [30/47286b] process > Mpileup (SRR7062655-13_1-18... [ 50%] 369 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2872) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [33/e58f9e] process > HaplotypeCaller (SRR7062655... [ 56%] 417 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 417 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [77/8682ca] process > FreebayesSingle (SRR7062655... [ 66%] 488 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [30/47286b] process > Mpileup (SRR7062655-13_1-18... [ 50%] 369 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2873) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [e1/17e0ba] process > HaplotypeCaller (SRR7062655... [ 56%] 417 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 417 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [77/8682ca] process > FreebayesSingle (SRR7062655... [ 66%] 488 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [30/47286b] process > Mpileup (SRR7062655-13_1-18... [ 50%] 369 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2874) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [0c/94a969] process > HaplotypeCaller (SRR7062655... [ 56%] 418 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 418 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [21/8b66d0] process > FreebayesSingle (SRR7062655... [ 66%] 488 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [30/47286b] process > Mpileup (SRR7062655-13_1-18... [ 50%] 369 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2875) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [10/1f6416] process > HaplotypeCaller (SRR7062655... [ 57%] 419 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 419 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [21/8b66d0] process > FreebayesSingle (SRR7062655... [ 66%] 488 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [30/47286b] process > Mpileup (SRR7062655-13_1-18... [ 50%] 369 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2876) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [5b/8825af] process > HaplotypeCaller (SRR7062655... [ 57%] 420 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 420 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6a/8dd10c] process > FreebayesSingle (SRR7062655... [ 66%] 488 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [30/47286b] process > Mpileup (SRR7062655-13_1-18... [ 50%] 369 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2878) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [06/34e212] process > HaplotypeCaller (SRR7062655... [ 57%] 422 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 422 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6a/8dd10c] process > FreebayesSingle (SRR7062655... [ 66%] 488 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [30/47286b] process > Mpileup (SRR7062655-13_1-18... [ 50%] 369 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2881) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [91/cd0519] process > HaplotypeCaller (SRR7062655... [ 58%] 426 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 426 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6a/8dd10c] process > FreebayesSingle (SRR7062655... [ 66%] 491 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [30/47286b] process > Mpileup (SRR7062655-13_1-18... [ 50%] 369 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2885) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [c3/139688] process > HaplotypeCaller (SRR7062655... [ 58%] 426 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 426 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [c0/77c311] process > FreebayesSingle (SRR7062655... [ 66%] 491 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [30/47286b] process > Mpileup (SRR7062655-13_1-18... [ 50%] 369 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2887) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [c0/686106] process > HaplotypeCaller (SRR7062655... [ 58%] 428 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 428 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [c0/77c311] process > FreebayesSingle (SRR7062655... [ 66%] 491 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [30/47286b] process > Mpileup (SRR7062655-13_1-18... [ 50%] 369 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2888) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [e0/f84184] process > HaplotypeCaller (SRR7062655... [ 58%] 429 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 429 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [c0/77c311] process > FreebayesSingle (SRR7062655... [ 66%] 491 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [30/47286b] process > Mpileup (SRR7062655-13_1-18... [ 50%] 369 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2890) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [4b/ac2b05] process > HaplotypeCaller (SRR7062655... [ 58%] 431 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 431 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [c0/77c311] process > FreebayesSingle (SRR7062655... [ 66%] 491 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [30/47286b] process > Mpileup (SRR7062655-13_1-18... [ 50%] 369 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2894) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [4b/d77789] process > HaplotypeCaller (SRR7062655... [ 59%] 435 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 435 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [88/49ad28] process > FreebayesSingle (SRR7062655... [ 66%] 491 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [30/47286b] process > Mpileup (SRR7062655-13_1-18... [ 50%] 369 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2895) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [9e/3a058b] process > HaplotypeCaller (SRR7062655... [ 59%] 436 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 436 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0a/220dc6] process > FreebayesSingle (SRR7062655... [ 66%] 491 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [30/47286b] process > Mpileup (SRR7062655-13_1-18... [ 50%] 369 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2895) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [9e/3a058b] process > HaplotypeCaller (SRR7062655... [ 59%] 436 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 436 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0a/220dc6] process > FreebayesSingle (SRR7062655... [ 66%] 491 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a9/4378de] process > Mpileup (SRR7062655-17_1-10... [ 50%] 370 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2898) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [1d/d3fc81] process > HaplotypeCaller (SRR7062655... [ 59%] 437 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 437 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [94/66e9b6] process > FreebayesSingle (SRR7062655... [ 66%] 492 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a9/4378de] process > Mpileup (SRR7062655-17_1-10... [ 50%] 370 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2898) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [27/280f6b] process > HaplotypeCaller (SRR7062655... [ 59%] 440 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 438 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [94/66e9b6] process > FreebayesSingle (SRR7062655... [ 66%] 492 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [20/6444ac] process > Mpileup (SRR7062655-20_1-14... [ 50%] 371 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2904) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [4b/654c9f] process > HaplotypeCaller (SRR7062655... [ 60%] 442 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 442 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [19/557fca] process > FreebayesSingle (SRR7062655... [ 67%] 494 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [20/6444ac] process > Mpileup (SRR7062655-20_1-14... [ 50%] 371 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2906) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [4b/654c9f] process > HaplotypeCaller (SRR7062655... [ 60%] 442 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 442 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [36/2453c3] process > FreebayesSingle (SRR7062655... [ 67%] 494 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [20/6444ac] process > Mpileup (SRR7062655-20_1-14... [ 50%] 371 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2907) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [b6/f3d5a6] process > HaplotypeCaller (SRR7062655... [ 60%] 443 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 443 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [00/7c0bb3] process > FreebayesSingle (SRR7062655... [ 67%] 494 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [20/6444ac] process > Mpileup (SRR7062655-20_1-14... [ 50%] 371 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2909) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [4b/d77789] process > HaplotypeCaller (SRR7062655... [ 60%] 446 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 446 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5b/eb92d8] process > FreebayesSingle (SRR7062655... [ 67%] 494 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [20/6444ac] process > Mpileup (SRR7062655-20_1-14... [ 50%] 371 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2910) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [4b/d77789] process > HaplotypeCaller (SRR7062655... [ 60%] 446 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 446 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [82/7dfc2a] process > FreebayesSingle (SRR7062655... [ 67%] 494 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [20/6444ac] process > Mpileup (SRR7062655-20_1-14... [ 50%] 371 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2911) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [e4/cf4c79] process > HaplotypeCaller (SRR7062655... [ 61%] 452 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 452 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a1/fd2864] process > FreebayesSingle (SRR7062655... [ 67%] 494 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [20/6444ac] process > Mpileup (SRR7062655-20_1-14... [ 50%] 371 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2916) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [c4/3064e0] process > HaplotypeCaller (SRR7062655... [ 61%] 452 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 452 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ff/bd5053] process > FreebayesSingle (SRR7062655... [ 67%] 494 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [20/6444ac] process > Mpileup (SRR7062655-20_1-14... [ 50%] 371 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2918) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [eb/dc7b42] process > HaplotypeCaller (SRR7062655... [ 61%] 454 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 454 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [8a/8c9faf] process > FreebayesSingle (SRR7062655... [ 68%] 501 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [20/6444ac] process > Mpileup (SRR7062655-20_1-14... [ 50%] 371 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2924) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [d9/801925] process > HaplotypeCaller (SRR7062655... [ 61%] 454 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 454 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f1/676427] process > FreebayesSingle (SRR7062655... [ 68%] 501 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [20/6444ac] process > Mpileup (SRR7062655-20_1-14... [ 50%] 371 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2925) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [22/5d37a8] process > HaplotypeCaller (SRR7062655... [ 61%] 454 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 454 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f1/676427] process > FreebayesSingle (SRR7062655... [ 68%] 501 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [20/6444ac] process > Mpileup (SRR7062655-20_1-14... [ 50%] 371 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2929) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [5a/e4af33] process > HaplotypeCaller (SRR7062655... [ 61%] 455 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 455 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [89/5f3674] process > FreebayesSingle (SRR7062655... [ 69%] 509 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [80/a68a45] process > Mpileup (SRR7062655-19_1-99... [ 50%] 372 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2935) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [5a/e4af33] process > HaplotypeCaller (SRR7062655... [ 61%] 455 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 455 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [75/15b333] process > FreebayesSingle (SRR7062655... [ 69%] 509 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [80/a68a45] process > Mpileup (SRR7062655-19_1-99... [ 50%] 372 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2936) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [5a/e4af33] process > HaplotypeCaller (SRR7062655... [ 61%] 455 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 455 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6e/2094a7] process > FreebayesSingle (SRR7062655... [ 69%] 509 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8f/c9392f] process > Mpileup (SRR7062655-12_1-19... [ 50%] 373 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2937) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [ad/8cadc5] process > HaplotypeCaller (SRR7062655... [ 62%] 456 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 456 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [cd/81fde1] process > FreebayesSingle (SRR7062655... [ 69%] 509 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8f/c9392f] process > Mpileup (SRR7062655-12_1-19... [ 50%] 373 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2938) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [c0/686106] process > HaplotypeCaller (SRR7062655... [ 62%] 457 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 457 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [68/9e79be] process > FreebayesSingle (SRR7062655... [ 69%] 509 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8f/c9392f] process > Mpileup (SRR7062655-12_1-19... [ 50%] 373 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2942) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [4b/654c9f] process > HaplotypeCaller (SRR7062655... [ 62%] 459 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 459 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ff/bbd7a6] process > FreebayesSingle (SRR7062655... [ 69%] 512 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8f/c9392f] process > Mpileup (SRR7062655-12_1-19... [ 50%] 373 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2943) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [4b/654c9f] process > HaplotypeCaller (SRR7062655... [ 62%] 459 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 459 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [fc/612de6] process > FreebayesSingle (SRR7062655... [ 69%] 512 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8f/c9392f] process > Mpileup (SRR7062655-12_1-19... [ 50%] 373 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2948) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [64/d07825] process > HaplotypeCaller (SRR7062655... [ 62%] 459 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 459 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [82/32e7e0] process > FreebayesSingle (SRR7062655... [ 70%] 521 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [03/e39513] process > Mpileup (SRR7062654-5_1-598... [ 51%] 374 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2953) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [64/d07825] process > HaplotypeCaller (SRR7062655... [ 62%] 459 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 459 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [03/6bfbae] process > FreebayesSingle (SRR7062655... [ 70%] 521 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [03/e39513] process > Mpileup (SRR7062654-5_1-598... [ 51%] 374 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2953) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [64/d07825] process > HaplotypeCaller (SRR7062655... [ 62%] 459 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 459 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [03/6bfbae] process > FreebayesSingle (SRR7062655... [ 70%] 521 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f4/ed0b39] process > Mpileup (SRR7062655-7_1-369... [ 51%] 375 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2959) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [33/1a48f5] process > HaplotypeCaller (SRR7062655... [ 62%] 460 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 460 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [75/15b333] process > FreebayesSingle (SRR7062655... [ 71%] 529 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f4/ed0b39] process > Mpileup (SRR7062655-7_1-369... [ 51%] 375 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2963) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [33/1a48f5] process > HaplotypeCaller (SRR7062655... [ 62%] 460 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 460 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [1a/19bd15] process > FreebayesSingle (SRR7062655... [ 71%] 529 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f4/ed0b39] process > Mpileup (SRR7062655-7_1-369... [ 51%] 375 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2964) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [1f/9db78c] process > HaplotypeCaller (SRR7062655... [ 62%] 461 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 461 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [1a/19bd15] process > FreebayesSingle (SRR7062655... [ 71%] 529 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f4/ed0b39] process > Mpileup (SRR7062655-7_1-369... [ 51%] 375 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2964) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [5a/e4af33] process > HaplotypeCaller (SRR7062655... [ 63%] 465 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 464 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [1a/19bd15] process > FreebayesSingle (SRR7062655... [ 71%] 529 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f4/ed0b39] process > Mpileup (SRR7062655-7_1-369... [ 51%] 375 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2968) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [98/b0413d] process > HaplotypeCaller (SRR7062655... [ 63%] 465 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 465 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2b/c03b64] process > FreebayesSingle (SRR7062655... [ 71%] 529 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f4/ed0b39] process > Mpileup (SRR7062655-7_1-369... [ 51%] 375 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2968) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [67/714657] process > HaplotypeCaller (SRR7062655... [ 63%] 467 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 467 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2b/c03b64] process > FreebayesSingle (SRR7062655... [ 71%] 529 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f4/ed0b39] process > Mpileup (SRR7062655-7_1-369... [ 51%] 375 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2970) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [21/98f482] process > HaplotypeCaller (SRR7062655... [ 63%] 467 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 467 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2b/c03b64] process > FreebayesSingle (SRR7062655... [ 71%] 529 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f4/ed0b39] process > Mpileup (SRR7062655-7_1-369... [ 51%] 375 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2971) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [5e/fad1ea] process > HaplotypeCaller (SRR7062655... [ 63%] 468 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 468 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ac/56aacf] process > FreebayesSingle (SRR7062655... [ 73%] 538 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f4/ed0b39] process > Mpileup (SRR7062655-7_1-369... [ 51%] 375 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2978) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [d0/c82330] process > HaplotypeCaller (SRR7062655... [ 63%] 468 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 468 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [20/483384] process > FreebayesSingle (SRR7062655... [ 73%] 541 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f4/ed0b39] process > Mpileup (SRR7062655-7_1-369... [ 51%] 375 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2983) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [b4/827686] process > HaplotypeCaller (SRR7062655... [ 63%] 468 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 468 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5d/e927d4] process > FreebayesSingle (SRR7062655... [ 73%] 541 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f4/ed0b39] process > Mpileup (SRR7062655-7_1-369... [ 51%] 375 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2985) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [40/f391fd] process > HaplotypeCaller (SRR7062655... [ 63%] 468 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 468 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [1a/19bd15] process > FreebayesSingle (SRR7062655... [ 74%] 549 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f4/ed0b39] process > Mpileup (SRR7062655-7_1-369... [ 51%] 375 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2991) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [a0/a804e2] process > HaplotypeCaller (SRR7062655... [ 63%] 468 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 468 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [c3/f38048] process > FreebayesSingle (SRR7062655... [ 74%] 549 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f4/ed0b39] process > Mpileup (SRR7062655-7_1-369... [ 51%] 375 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2992) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [87/f8faa8] process > HaplotypeCaller (SRR7062655... [ 63%] 468 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 468 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2b/c03b64] process > FreebayesSingle (SRR7062655... [ 74%] 550 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f4/ed0b39] process > Mpileup (SRR7062655-7_1-369... [ 51%] 375 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2993) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [35/00c72a] process > HaplotypeCaller (SRR7062655... [ 63%] 469 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 469 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0d/bf01fa] process > FreebayesSingle (SRR7062655... [ 74%] 550 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f4/ed0b39] process > Mpileup (SRR7062655-7_1-369... [ 51%] 375 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2996) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [3b/f0f0ee] process > HaplotypeCaller (SRR7062655... [ 64%] 472 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 472 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [03/d51996] process > FreebayesSingle (SRR7062655... [ 74%] 550 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f4/ed0b39] process > Mpileup (SRR7062655-7_1-369... [ 51%] 375 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (2998) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [29/75b595] process > HaplotypeCaller (SRR7062655... [ 64%] 476 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 476 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/73940d] process > FreebayesSingle (SRR7062655... [ 74%] 550 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f4/ed0b39] process > Mpileup (SRR7062655-7_1-369... [ 51%] 375 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3000) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [29/75b595] process > HaplotypeCaller (SRR7062655... [ 64%] 476 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 476 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [22/73b7a7] process > FreebayesSingle (SRR7062655... [ 74%] 550 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f4/ed0b39] process > Mpileup (SRR7062655-7_1-369... [ 51%] 375 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3003) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [00/1f0504] process > HaplotypeCaller (SRR7062655... [ 65%] 480 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 480 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [03/d51996] process > FreebayesSingle (SRR7062655... [ 75%] 555 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f4/ed0b39] process > Mpileup (SRR7062655-7_1-369... [ 51%] 375 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3009) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [0e/97684a] process > HaplotypeCaller (SRR7062655... [ 65%] 480 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 480 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [03/d51996] process > FreebayesSingle (SRR7062655... [ 75%] 555 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f4/ed0b39] process > Mpileup (SRR7062655-7_1-369... [ 51%] 375 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3011) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [31/123bec] process > HaplotypeCaller (SRR7062655... [ 65%] 480 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 480 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5d/e927d4] process > FreebayesSingle (SRR7062655... [ 75%] 557 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f4/ed0b39] process > Mpileup (SRR7062655-7_1-369... [ 51%] 375 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3012) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [18/a1dd32] process > HaplotypeCaller (SRR7062655... [ 65%] 480 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 480 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [90/21727d] process > FreebayesSingle (SRR7062655... [ 75%] 558 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f4/ed0b39] process > Mpileup (SRR7062655-7_1-369... [ 51%] 375 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3016) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [cb/032d8f] process > HaplotypeCaller (SRR7062655... [ 65%] 483 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 483 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [90/21727d] process > FreebayesSingle (SRR7062655... [ 75%] 558 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1b/fd27ff] process > Mpileup (SRR7062655-15_1-12... [ 51%] 376 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3019) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [33/4da333] process > HaplotypeCaller (SRR7062655... [ 66%] 489 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 489 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [90/21727d] process > FreebayesSingle (SRR7062655... [ 75%] 558 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2f/dfaf01] process > Mpileup (SRR7062655-10_1-20... [ 51%] 377 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3023) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [6b/53b9d4] process > HaplotypeCaller (SRR7062655... [ 66%] 489 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 489 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [d8/a471f0] process > FreebayesSingle (SRR7062655... [ 75%] 558 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2f/dfaf01] process > Mpileup (SRR7062655-10_1-20... [ 51%] 377 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3027) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [43/66be2d] process > HaplotypeCaller (SRR7062655... [ 67%] 494 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 494 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [46/a01077] process > FreebayesSingle (SRR7062655... [ 76%] 560 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2f/dfaf01] process > Mpileup (SRR7062655-10_1-20... [ 51%] 377 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3030) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [43/66be2d] process > HaplotypeCaller (SRR7062655... [ 67%] 494 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 494 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f7/beb6dd] process > FreebayesSingle (SRR7062655... [ 76%] 560 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2f/dfaf01] process > Mpileup (SRR7062655-10_1-20... [ 51%] 377 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3030) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [1e/5b3479] process > HaplotypeCaller (SRR7062655... [ 67%] 495 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 495 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f7/beb6dd] process > FreebayesSingle (SRR7062655... [ 76%] 560 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2f/dfaf01] process > Mpileup (SRR7062655-10_1-20... [ 51%] 377 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3033) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [5a/dfba84] process > HaplotypeCaller (SRR7062655... [ 67%] 496 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 496 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [63/a4a62a] process > FreebayesSingle (SRR7062655... [ 76%] 561 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2f/dfaf01] process > Mpileup (SRR7062655-10_1-20... [ 51%] 377 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3033) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [51/cbbc8a] process > HaplotypeCaller (SRR7062655... [ 67%] 498 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 498 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [63/a4a62a] process > FreebayesSingle (SRR7062655... [ 76%] 561 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2f/dfaf01] process > Mpileup (SRR7062655-10_1-20... [ 51%] 377 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3035) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [51/cbbc8a] process > HaplotypeCaller (SRR7062655... [ 67%] 498 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 498 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [24/5fe462] process > FreebayesSingle (SRR7062655... [ 76%] 561 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2f/dfaf01] process > Mpileup (SRR7062655-10_1-20... [ 51%] 377 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3036) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [da/48bd63] process > HaplotypeCaller (SRR7062655... [ 67%] 499 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 499 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [72/ab7ede] process > FreebayesSingle (SRR7062655... [ 76%] 561 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2f/dfaf01] process > Mpileup (SRR7062655-10_1-20... [ 51%] 377 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3037) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [6c/2cade9] process > HaplotypeCaller (SRR7062655... [ 68%] 502 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 502 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [be/b0c029] process > FreebayesSingle (SRR7062655... [ 76%] 561 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cc/f54be7] process > Mpileup (SRR7062655-18_1-11... [ 51%] 378 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3040) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [6c/2cade9] process > HaplotypeCaller (SRR7062655... [ 68%] 502 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 502 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ff/f140f1] process > FreebayesSingle (SRR7062655... [ 76%] 561 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cc/f54be7] process > Mpileup (SRR7062655-18_1-11... [ 51%] 378 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3040) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [e2/fb7eb6] process > HaplotypeCaller (SRR7062655... [ 68%] 504 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 503 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ff/f140f1] process > FreebayesSingle (SRR7062655... [ 76%] 561 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cc/f54be7] process > Mpileup (SRR7062655-18_1-11... [ 51%] 378 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3044) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [82/f742f6] process > HaplotypeCaller (SRR7062655... [ 69%] 508 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 508 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ba/4ae68f] process > FreebayesSingle (SRR7062655... [ 76%] 561 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cc/f54be7] process > Mpileup (SRR7062655-18_1-11... [ 51%] 378 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3046) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [82/f742f6] process > HaplotypeCaller (SRR7062655... [ 69%] 508 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 508 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [fe/053b5e] process > FreebayesSingle (SRR7062655... [ 76%] 561 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cc/f54be7] process > Mpileup (SRR7062655-18_1-11... [ 51%] 378 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3046) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [31/123bec] process > HaplotypeCaller (SRR7062655... [ 69%] 511 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 511 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [fe/053b5e] process > FreebayesSingle (SRR7062655... [ 76%] 561 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cc/f54be7] process > Mpileup (SRR7062655-18_1-11... [ 51%] 378 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3052) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [cb/032d8f] process > HaplotypeCaller (SRR7062655... [ 69%] 512 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 512 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [29/23ed4a] process > FreebayesSingle (SRR7062655... [ 76%] 565 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cc/f54be7] process > Mpileup (SRR7062655-18_1-11... [ 51%] 378 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3054) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [cb/032d8f] process > HaplotypeCaller (SRR7062655... [ 69%] 512 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 512 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f8/7b681b] process > FreebayesSingle (SRR7062655... [ 76%] 565 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cc/f54be7] process > Mpileup (SRR7062655-18_1-11... [ 51%] 378 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3055) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [cb/15909c] process > HaplotypeCaller (SRR7062655... [ 69%] 513 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 513 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b0/7cb621] process > FreebayesSingle (SRR7062655... [ 77%] 571 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cc/f54be7] process > Mpileup (SRR7062655-18_1-11... [ 51%] 378 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3062) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [cb/15909c] process > HaplotypeCaller (SRR7062655... [ 69%] 513 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 513 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [de/f0945a] process > FreebayesSingle (SRR7062655... [ 78%] 578 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cc/f54be7] process > Mpileup (SRR7062655-18_1-11... [ 51%] 378 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3067) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [cb/15909c] process > HaplotypeCaller (SRR7062655... [ 69%] 513 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 513 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [8a/5d9466] process > FreebayesSingle (SRR7062655... [ 78%] 578 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cc/f54be7] process > Mpileup (SRR7062655-18_1-11... [ 51%] 378 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3068) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [cb/15909c] process > HaplotypeCaller (SRR7062655... [ 69%] 513 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 513 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [00/b3e661] process > FreebayesSingle (SRR7062655... [ 78%] 578 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cc/f54be7] process > Mpileup (SRR7062655-18_1-11... [ 51%] 378 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3070) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [ec/23763b] process > HaplotypeCaller (SRR7062655... [ 70%] 515 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 515 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [00/b3e661] process > FreebayesSingle (SRR7062655... [ 78%] 578 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cc/f54be7] process > Mpileup (SRR7062655-18_1-11... [ 51%] 378 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3071) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [10/3076fe] process > HaplotypeCaller (SRR7062655... [ 70%] 516 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 516 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b5/eff753] process > FreebayesSingle (SRR7062655... [ 78%] 578 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cc/f54be7] process > Mpileup (SRR7062655-18_1-11... [ 51%] 378 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3072) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [d6/1bcf23] process > HaplotypeCaller (SRR7062655... [ 70%] 519 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 519 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b5/eff753] process > FreebayesSingle (SRR7062655... [ 78%] 578 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cc/f54be7] process > Mpileup (SRR7062655-18_1-11... [ 51%] 378 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3074) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [b1/04bdf5] process > HaplotypeCaller (SRR7062655... [ 70%] 519 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 519 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e6/a8ecc6] process > FreebayesSingle (SRR7062655... [ 78%] 578 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cc/f54be7] process > Mpileup (SRR7062655-18_1-11... [ 51%] 378 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3076) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [17/a69b22] process > HaplotypeCaller (SRR7062655... [ 70%] 520 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 520 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [88/e3f0a6] process > FreebayesSingle (SRR7062655... [ 79%] 587 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cc/f54be7] process > Mpileup (SRR7062655-18_1-11... [ 51%] 378 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3083) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [6d/237915] process > HaplotypeCaller (SRR7062655... [ 70%] 520 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 520 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [cc/dd5ca2] process > FreebayesSingle (SRR7062655... [ 80%] 593 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cc/f54be7] process > Mpileup (SRR7062655-18_1-11... [ 51%] 378 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3089) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [4f/fdc978] process > HaplotypeCaller (SRR7062655... [ 70%] 520 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 520 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [27/76e552] process > FreebayesSingle (SRR7062655... [ 80%] 593 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cc/f54be7] process > Mpileup (SRR7062655-18_1-11... [ 51%] 378 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3090) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [4f/fdc978] process > HaplotypeCaller (SRR7062655... [ 70%] 520 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 520 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [84/448d9e] process > FreebayesSingle (SRR7062655... [ 80%] 593 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cc/f54be7] process > Mpileup (SRR7062655-18_1-11... [ 51%] 378 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3092) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [33/4da333] process > HaplotypeCaller (SRR7062655... [ 70%] 521 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 521 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [02/21325e] process > FreebayesSingle (SRR7062655... [ 81%] 603 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/f9eadf] process > Mpileup (SRR7062655-11_1-20... [ 51%] 379 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3097) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [58/7a7af3] process > HaplotypeCaller (SRR7062655... [ 70%] 521 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 521 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/478f6e] process > FreebayesSingle (SRR7062655... [ 81%] 603 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/f9eadf] process > Mpileup (SRR7062655-11_1-20... [ 51%] 379 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3102) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [05/70e313] process > HaplotypeCaller (SRR7062655... [ 70%] 521 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 521 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [37/478f6e] process > FreebayesSingle (SRR7062655... [ 81%] 603 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/f9eadf] process > Mpileup (SRR7062655-11_1-20... [ 51%] 379 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3106) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [ab/248d38] process > HaplotypeCaller (SRR7062655... [ 70%] 521 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 521 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [27/2e84f9] process > FreebayesSingle (SRR7062655... [ 82%] 607 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/f9eadf] process > Mpileup (SRR7062655-11_1-20... [ 51%] 379 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3107) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [cd/02cb64] process > HaplotypeCaller (SRR7062655... [ 71%] 522 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 522 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [27/2e84f9] process > FreebayesSingle (SRR7062655... [ 82%] 607 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/f9eadf] process > Mpileup (SRR7062655-11_1-20... [ 51%] 379 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3108) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [50/984692] process > HaplotypeCaller (SRR7062655... [ 71%] 523 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 523 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2d/3e6bcc] process > FreebayesSingle (SRR7062655... [ 82%] 607 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/f9eadf] process > Mpileup (SRR7062655-11_1-20... [ 51%] 379 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3110) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [41/5d6f84] process > HaplotypeCaller (SRR7062655... [ 71%] 525 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 525 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2d/3e6bcc] process > FreebayesSingle (SRR7062655... [ 82%] 607 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/f9eadf] process > Mpileup (SRR7062655-11_1-20... [ 51%] 379 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3110) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [41/5d6f84] process > HaplotypeCaller (SRR7062655... [ 71%] 525 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 525 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2d/3e6bcc] process > FreebayesSingle (SRR7062655... [ 82%] 607 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/f9eadf] process > Mpileup (SRR7062655-11_1-20... [ 51%] 379 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3115) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [29/c09f2c] process > HaplotypeCaller (SRR7062655... [ 71%] 526 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 526 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [88/09f10f] process > FreebayesSingle (SRR7062655... [ 83%] 611 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/f9eadf] process > Mpileup (SRR7062655-11_1-20... [ 51%] 379 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3119) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [26/f5332e] process > HaplotypeCaller (SRR7062655... [ 71%] 526 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 526 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [88/0e9305] process > FreebayesSingle (SRR7062655... [ 84%] 620 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/f9eadf] process > Mpileup (SRR7062655-11_1-20... [ 51%] 379 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3124) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [c0/b9c715] process > HaplotypeCaller (SRR7062655... [ 71%] 526 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 526 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [43/93e104] process > FreebayesSingle (SRR7062655... [ 84%] 620 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/f9eadf] process > Mpileup (SRR7062655-11_1-20... [ 51%] 379 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3124) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [c0/b9c715] process > HaplotypeCaller (SRR7062655... [ 71%] 526 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 526 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e0/5443f2] process > FreebayesSingle (SRR7062654... [ 84%] 621 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/f9eadf] process > Mpileup (SRR7062655-11_1-20... [ 51%] 379 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3125) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [c0/b9c715] process > HaplotypeCaller (SRR7062655... [ 71%] 526 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 526 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [00/735734] process > FreebayesSingle (SRR7062655... [ 84%] 621 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/f9eadf] process > Mpileup (SRR7062655-11_1-20... [ 51%] 379 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3125) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [c0/b9c715] process > HaplotypeCaller (SRR7062655... [ 71%] 526 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 526 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [30/2dbf25] process > FreebayesSingle (SRR7062655... [ 84%] 622 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/f9eadf] process > Mpileup (SRR7062655-11_1-20... [ 51%] 379 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3126) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [c0/b9c715] process > HaplotypeCaller (SRR7062655... [ 71%] 526 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 526 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [88/9c1425] process > FreebayesSingle (SRR7062655... [ 84%] 622 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/f9eadf] process > Mpileup (SRR7062655-11_1-20... [ 51%] 379 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3126) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [ab/248d38] process > HaplotypeCaller (SRR7062655... [ 71%] 528 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 528 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [88/9c1425] process > FreebayesSingle (SRR7062655... [ 84%] 622 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/f9eadf] process > Mpileup (SRR7062655-11_1-20... [ 51%] 379 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3128) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [1f/dcc006] process > HaplotypeCaller (SRR7062655... [ 71%] 528 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 528 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [fa/f75213] process > FreebayesSingle (SRR7062655... [ 84%] 622 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/f9eadf] process > Mpileup (SRR7062655-11_1-20... [ 51%] 379 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3128) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [ac/10afdb] process > HaplotypeCaller (SRR7062655... [ 72%] 530 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 530 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [fa/f75213] process > FreebayesSingle (SRR7062655... [ 84%] 622 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/f9eadf] process > Mpileup (SRR7062655-11_1-20... [ 51%] 379 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3132) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [a0/78c2ee] process > HaplotypeCaller (SRR7062655... [ 73%] 537 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 537 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ae/ef51ac] process > FreebayesSingle (SRR7062655... [ 84%] 622 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/f9eadf] process > Mpileup (SRR7062655-11_1-20... [ 51%] 379 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3137) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [82/13e4b7] process > HaplotypeCaller (SRR7062655... [ 73%] 537 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 537 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b5/c90b0c] process > FreebayesSingle (SRR7062655... [ 84%] 622 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/f9eadf] process > Mpileup (SRR7062655-11_1-20... [ 51%] 379 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3138) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [58/7a7af3] process > HaplotypeCaller (SRR7062655... [ 73%] 542 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 541 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b5/c90b0c] process > FreebayesSingle (SRR7062655... [ 84%] 622 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/f9eadf] process > Mpileup (SRR7062655-11_1-20... [ 51%] 379 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3143) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [81/36f31a] process > HaplotypeCaller (SRR7062655... [ 74%] 544 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 544 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [fa/f75213] process > FreebayesSingle (SRR7062655... [ 85%] 626 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/f9eadf] process > Mpileup (SRR7062655-11_1-20... [ 51%] 379 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3148) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [ab/381deb] process > HaplotypeCaller (SRR7062655... [ 74%] 544 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 544 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [fa/f75213] process > FreebayesSingle (SRR7062655... [ 85%] 626 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/f9eadf] process > Mpileup (SRR7062655-11_1-20... [ 51%] 379 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3149) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [a1/68b6b9] process > HaplotypeCaller (SRR7062655... [ 74%] 546 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 546 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [88/9c1425] process > FreebayesSingle (SRR7062655... [ 85%] 627 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/f9eadf] process > Mpileup (SRR7062655-11_1-20... [ 51%] 379 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3151) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [9c/afd92f] process > HaplotypeCaller (SRR7062655... [ 74%] 546 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 546 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [88/9c1425] process > FreebayesSingle (SRR7062655... [ 85%] 627 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/f9eadf] process > Mpileup (SRR7062655-11_1-20... [ 51%] 379 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3153) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [d2/e6c07f] process > HaplotypeCaller (SRR7062655... [ 74%] 546 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 546 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [00/735734] process > FreebayesSingle (SRR7062655... [ 85%] 628 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f9/ec076d] process > Mpileup (SRR7062655-8_1-299... [ 51%] 380 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3154) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [d4/68fac7] process > HaplotypeCaller (SRR7062655... [ 74%] 547 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 547 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [00/735734] process > FreebayesSingle (SRR7062655... [ 85%] 628 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f9/ec076d] process > Mpileup (SRR7062655-8_1-299... [ 51%] 380 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3157) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [60/b93296] process > HaplotypeCaller (SRR7062655... [ 75%] 552 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 552 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [97/9c6eec] process > FreebayesSingle (SRR7062655... [ 85%] 628 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f9/ec076d] process > Mpileup (SRR7062655-8_1-299... [ 51%] 380 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3159) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [60/b93296] process > HaplotypeCaller (SRR7062655... [ 75%] 552 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 552 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e6/aff965] process > FreebayesSingle (SRR7062655... [ 85%] 628 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f9/ec076d] process > Mpileup (SRR7062655-8_1-299... [ 51%] 380 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3162) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [1f/dcc006] process > HaplotypeCaller (SRR7062655... [ 75%] 557 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 557 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b8/3bb48c] process > FreebayesSingle (SRR7062655... [ 85%] 628 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f9/ec076d] process > Mpileup (SRR7062655-8_1-299... [ 51%] 380 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3164) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [1f/dcc006] process > HaplotypeCaller (SRR7062655... [ 75%] 557 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 557 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/afad88] process > FreebayesSingle (SRR7062655... [ 85%] 628 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f9/ec076d] process > Mpileup (SRR7062655-8_1-299... [ 51%] 380 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3168) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [88/51522e] process > HaplotypeCaller (SRR7062655... [ 76%] 562 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 562 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [c3/b28d64] process > FreebayesSingle (SRR7062655... [ 85%] 629 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f9/ec076d] process > Mpileup (SRR7062655-8_1-299... [ 51%] 380 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3170) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [88/51522e] process > HaplotypeCaller (SRR7062655... [ 76%] 562 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 562 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [75/d4ced3] process > FreebayesSingle (SRR7062655... [ 85%] 629 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f9/ec076d] process > Mpileup (SRR7062655-8_1-299... [ 51%] 380 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3175) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [88/51522e] process > HaplotypeCaller (SRR7062655... [ 76%] 562 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 562 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/8a0144] process > FreebayesSingle (SRR7062655... [ 86%] 635 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f9/ec076d] process > Mpileup (SRR7062655-8_1-299... [ 51%] 380 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3176) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [88/51522e] process > HaplotypeCaller (SRR7062655... [ 76%] 562 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 562 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9c/c01c3e] process > FreebayesSingle (SRR7062655... [ 86%] 635 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f9/ec076d] process > Mpileup (SRR7062655-8_1-299... [ 51%] 380 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3176) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [3c/dfa6a4] process > HaplotypeCaller (SRR7062655... [ 76%] 563 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 563 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [9c/c01c3e] process > FreebayesSingle (SRR7062655... [ 86%] 635 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f9/ec076d] process > Mpileup (SRR7062655-8_1-299... [ 51%] 380 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3177) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [3c/dfa6a4] process > HaplotypeCaller (SRR7062655... [ 76%] 563 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 563 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [d6/3c8c24] process > FreebayesSingle (SRR7062655... [ 86%] 635 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f9/ec076d] process > Mpileup (SRR7062655-8_1-299... [ 51%] 380 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3177) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [a0/78c2ee] process > HaplotypeCaller (SRR7062655... [ 76%] 566 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 565 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [d6/3c8c24] process > FreebayesSingle (SRR7062655... [ 86%] 635 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f9/ec076d] process > Mpileup (SRR7062655-8_1-299... [ 51%] 380 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3182) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [d4/68fac7] process > HaplotypeCaller (SRR7062655... [ 77%] 568 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 568 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ef/c0e377] process > FreebayesSingle (SRR7062655... [ 86%] 635 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f9/ec076d] process > Mpileup (SRR7062655-8_1-299... [ 51%] 380 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3183) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [9c/afd92f] process > HaplotypeCaller (SRR7062655... [ 77%] 571 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 571 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [8c/44d9d8] process > FreebayesSingle (SRR7062655... [ 86%] 635 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f9/ec076d] process > Mpileup (SRR7062655-8_1-299... [ 51%] 380 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3185) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [9c/afd92f] process > HaplotypeCaller (SRR7062655... [ 77%] 571 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 571 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [24/0cb321] process > FreebayesSingle (SRR7062655... [ 86%] 635 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f9/ec076d] process > Mpileup (SRR7062655-8_1-299... [ 51%] 380 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3186) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [60/b93296] process > HaplotypeCaller (SRR7062655... [ 78%] 576 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 576 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [86/268670] process > FreebayesSingle (SRR7062655... [ 86%] 635 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f9/ec076d] process > Mpileup (SRR7062655-8_1-299... [ 51%] 380 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3192) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [60/b93296] process > HaplotypeCaller (SRR7062655... [ 78%] 576 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 576 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [e1/64d232] process > FreebayesSingle (SRR7062655... [ 87%] 644 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f9/ec076d] process > Mpileup (SRR7062655-8_1-299... [ 51%] 380 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3197) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [61/e04ebc] process > HaplotypeCaller (SRR7062655... [ 78%] 576 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 576 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [36/8b5494] process > FreebayesSingle (SRR7062655... [ 87%] 644 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f9/ec076d] process > Mpileup (SRR7062655-8_1-299... [ 51%] 380 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3199) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [61/e04ebc] process > HaplotypeCaller (SRR7062655... [ 78%] 576 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 576 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0d/0de9aa] process > FreebayesSingle (SRR7062655... [ 87%] 644 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f9/ec076d] process > Mpileup (SRR7062655-8_1-299... [ 51%] 380 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3201) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [27/52333f] process > HaplotypeCaller (SRR7062655... [ 78%] 579 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 579 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [c3/b28d64] process > FreebayesSingle (SRR7062655... [ 88%] 650 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a3/a87518] process > Mpileup (SRR7062655-5_1-598... [ 52%] 382 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3207) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [a6/3bf499] process > HaplotypeCaller (SRR7062655... [ 78%] 579 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 579 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [bf/445d92] process > FreebayesSingle (SRR7062655... [ 89%] 655 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a3/a87518] process > Mpileup (SRR7062655-5_1-598... [ 52%] 382 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3213) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [fa/4349d7] process > HaplotypeCaller (SRR7062655... [ 78%] 579 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 579 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [c4/2951ab] process > FreebayesSingle (SRR7062655... [ 89%] 655 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a3/a87518] process > Mpileup (SRR7062655-5_1-598... [ 52%] 382 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3215) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [34/46c155] process > HaplotypeCaller (SRR7062655... [ 78%] 579 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 579 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/af7c45] process > FreebayesSingle (SRR7062655... [ 89%] 655 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a3/a87518] process > Mpileup (SRR7062655-5_1-598... [ 52%] 382 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3217) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [21/628e30] process > HaplotypeCaller (SRR7062655... [ 79%] 582 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 582 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ba/b86208] process > FreebayesSingle (SRR7062655... [ 89%] 658 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a3/a87518] process > Mpileup (SRR7062655-5_1-598... [ 52%] 382 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3221) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [42/4d17d9] process > HaplotypeCaller (SRR7062655... [ 79%] 582 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 582 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3d/bf3c87] process > FreebayesSingle (SRR7062655... [ 89%] 658 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a3/a87518] process > Mpileup (SRR7062655-5_1-598... [ 52%] 382 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3223) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [a1/fc0070] process > HaplotypeCaller (SRR7062655... [ 79%] 584 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 584 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2f/e47041] process > FreebayesSingle (SRR7062655... [ 89%] 658 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a3/a87518] process > Mpileup (SRR7062655-5_1-598... [ 52%] 382 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3224) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [c2/5dae5f] process > HaplotypeCaller (SRR7062655... [ 79%] 584 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 584 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2f/e47041] process > FreebayesSingle (SRR7062655... [ 89%] 658 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c6/836c22] process > Mpileup (SRR7062655-9_1-240... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3225) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [e2/143e4a] process > HaplotypeCaller (SRR7062655... [ 79%] 585 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 585 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2f/e47041] process > FreebayesSingle (SRR7062655... [ 89%] 658 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c6/836c22] process > Mpileup (SRR7062655-9_1-240... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3225) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [e2/143e4a] process > HaplotypeCaller (SRR7062655... [ 79%] 585 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 585 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2f/e47041] process > FreebayesSingle (SRR7062655... [ 89%] 658 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c6/836c22] process > Mpileup (SRR7062655-9_1-240... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3228) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [88/cd9503] process > HaplotypeCaller (SRR7062655... [ 79%] 586 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 586 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [62/bb005e] process > FreebayesSingle (SRR7062655... [ 90%] 669 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c6/836c22] process > Mpileup (SRR7062655-9_1-240... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3234) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [ae/d49057] process > HaplotypeCaller (SRR7062655... [ 79%] 586 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 586 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [62/bb005e] process > FreebayesSingle (SRR7062655... [ 90%] 669 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [51/2af203] process > Mpileup (SRR7062655-AADN040... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3237) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [ae/d49057] process > HaplotypeCaller (SRR7062655... [ 79%] 586 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 586 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [62/bb005e] process > FreebayesSingle (SRR7062655... [ 90%] 669 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [46/9553c6] process > Mpileup (SRR7062655-AADN040... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3241) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [ae/d49057] process > HaplotypeCaller (SRR7062655... [ 79%] 586 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 586 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [2f/e47041] process > FreebayesSingle (SRR7062655... [ 92%] 681 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [10/02824d] process > Mpileup (SRR7062655-KQ75946... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3248) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [20/f67b5f] process > HaplotypeCaller (SRR7062655... [ 79%] 586 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 586 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3a/020863] process > FreebayesSingle (SRR7062655... [ 92%] 681 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [22/cc268b] process > Mpileup (SRR7062655-AADN040... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3249) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [20/f67b5f] process > HaplotypeCaller (SRR7062655... [ 79%] 586 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 586 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3a/020863] process > FreebayesSingle (SRR7062655... [ 92%] 681 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b6/390c5f] process > Mpileup (SRR7062655-AADN040... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3254) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [a6/46d0a3] process > HaplotypeCaller (SRR7062654... [ 79%] 587 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 587 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3a/0863d2] process > FreebayesSingle (SRR7062655... [ 93%] 686 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2c/a4dbe8] process > Mpileup (SRR7062655-AADN040... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3255) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [a6/46d0a3] process > HaplotypeCaller (SRR7062654... [ 79%] 587 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 587 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3a/0863d2] process > FreebayesSingle (SRR7062655... [ 93%] 686 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fe/c023dc] process > Mpileup (SRR7062655-KQ75952... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3256) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [ 50%] 1 of 2 [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [97/6c7d74] process > HaplotypeCaller (SRR7062655... [ 79%] 588 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 588 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3a/0863d2] process > FreebayesSingle (SRR7062655... [ 93%] 686 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a0/b71f5d] process > Mpileup (SRR7062655-33_1-16... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3256) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [97/6c7d74] process > HaplotypeCaller (SRR7062655... [ 79%] 588 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 588 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3a/0863d2] process > FreebayesSingle (SRR7062655... [ 93%] 686 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a0/b71f5d] process > Mpileup (SRR7062655-33_1-16... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3258) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [e1/0be3d7] process > HaplotypeCaller (SRR7062655... [ 80%] 589 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 589 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3a/0863d2] process > FreebayesSingle (SRR7062655... [ 93%] 686 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2f/30eb6b] process > Mpileup (SRR7062655-KQ75940... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3258) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [42/4d17d9] process > HaplotypeCaller (SRR7062655... [ 80%] 591 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 591 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3a/0863d2] process > FreebayesSingle (SRR7062655... [ 93%] 686 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2f/30eb6b] process > Mpileup (SRR7062655-KQ75940... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3260) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [f6/4aba19] process > HaplotypeCaller (SRR7062655... [ 80%] 591 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 591 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3a/0863d2] process > FreebayesSingle (SRR7062655... [ 93%] 686 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [36/78fc48] process > Mpileup (SRR7062655-25_1-29... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3260) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [a6/3bf499] process > HaplotypeCaller (SRR7062655... [ 80%] 594 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 592 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3a/0863d2] process > FreebayesSingle (SRR7062655... [ 93%] 686 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [36/78fc48] process > Mpileup (SRR7062655-25_1-29... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3263) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [3b/d99de2] process > HaplotypeCaller (SRR7062655... [ 81%] 596 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 596 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [51/bc62ce] process > FreebayesSingle (SRR7062655... [ 93%] 687 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [36/78fc48] process > Mpileup (SRR7062655-25_1-29... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3266) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [7d/72337c] process > HaplotypeCaller (SRR7062655... [ 81%] 596 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 596 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/bf8dba] process > FreebayesSingle (SRR7062655... [ 93%] 687 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [36/78fc48] process > Mpileup (SRR7062655-25_1-29... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3267) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [77/f156f4] process > HaplotypeCaller (SRR7062655... [ 81%] 598 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 598 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3a/020863] process > FreebayesSingle (SRR7062655... [ 93%] 690 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [36/78fc48] process > Mpileup (SRR7062655-25_1-29... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3271) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [e1/406234] process > HaplotypeCaller (SRR7062655... [ 81%] 598 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 598 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [86/9a74b0] process > FreebayesSingle (SRR7062655... [ 93%] 690 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b0/b7699b] process > Mpileup (SRR7062655-AADN040... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3273) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [65/8c0232] process > HaplotypeCaller (SRR7062655... [ 81%] 599 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 599 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a5/db0e68] process > FreebayesSingle (SRR7062655... [ 93%] 691 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1a/bdd3c5] process > Mpileup (SRR7062655-AADN040... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3274) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [31/5f5365] process > HaplotypeCaller (SRR7062655... [ 81%] 600 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 600 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a5/db0e68] process > FreebayesSingle (SRR7062655... [ 93%] 691 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1a/bdd3c5] process > Mpileup (SRR7062655-AADN040... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3275) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [54/2890c7] process > HaplotypeCaller (SRR7062655... [ 82%] 605 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 605 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a5/db0e68] process > FreebayesSingle (SRR7062655... [ 93%] 691 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1a/bdd3c5] process > Mpileup (SRR7062655-AADN040... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3279) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [09/e2000a] process > HaplotypeCaller (SRR7062655... [ 82%] 605 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 605 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [a5/db0e68] process > FreebayesSingle (SRR7062655... [ 93%] 691 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1a/bdd3c5] process > Mpileup (SRR7062655-AADN040... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3281) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [d5/0011e6] process > HaplotypeCaller (SRR7062655... [ 82%] 606 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 606 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [34/2ced72] process > FreebayesSingle (SRR7062655... [ 94%] 692 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8d/b073fc] process > Mpileup (SRR7062655-21_1-68... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3284) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [9b/b191f9] process > HaplotypeCaller (SRR7062655... [ 82%] 608 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 608 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [86/9a74b0] process > FreebayesSingle (SRR7062655... [ 94%] 696 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8d/b073fc] process > Mpileup (SRR7062655-21_1-68... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3287) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [e5/e3f8ea] process > HaplotypeCaller (SRR7062655... [ 82%] 608 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 608 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0e/ba373a] process > FreebayesSingle (SRR7062655... [ 94%] 696 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8d/b073fc] process > Mpileup (SRR7062655-21_1-68... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3289) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [09/745387] process > HaplotypeCaller (SRR7062655... [ 82%] 610 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 610 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0e/ba373a] process > FreebayesSingle (SRR7062655... [ 94%] 696 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8d/b073fc] process > Mpileup (SRR7062655-21_1-68... [ 52%] 383 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3290) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [0a/290422] process > HaplotypeCaller (SRR7062655... [ 82%] 610 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 610 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0e/ba373a] process > FreebayesSingle (SRR7062655... [ 94%] 696 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3292) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [bd/3b6acc] process > HaplotypeCaller (SRR7062655... [ 83%] 612 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 612 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0e/ba373a] process > FreebayesSingle (SRR7062655... [ 94%] 696 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3294) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [a6/d21c8e] process > HaplotypeCaller (SRR7062655... [ 83%] 613 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 613 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0e/ba373a] process > FreebayesSingle (SRR7062655... [ 94%] 697 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3297) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [38/fe06f5] process > HaplotypeCaller (SRR7062655... [ 83%] 616 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 616 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [12/71768c] process > FreebayesSingle (SRR7062655... [ 94%] 697 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3299) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [ff/566efb] process > HaplotypeCaller (SRR7062655... [ 84%] 618 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 618 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5d/11080d] process > FreebayesSingle (SRR7062655... [ 94%] 697 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3303) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [61/d26d61] process > HaplotypeCaller (SRR7062655... [ 84%] 623 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 623 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5d/11080d] process > FreebayesSingle (SRR7062655... [ 94%] 697 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3304) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [61/d26d61] process > HaplotypeCaller (SRR7062655... [ 84%] 623 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 623 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [c2/c19e92] process > FreebayesSingle (SRR7062655... [ 94%] 697 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3306) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [09/e2000a] process > HaplotypeCaller (SRR7062655... [ 84%] 625 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 625 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [05/75a643] process > FreebayesSingle (SRR7062655... [ 94%] 697 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3306) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [7c/ba44f4] process > HaplotypeCaller (SRR7062655... [ 85%] 626 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 625 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [05/75a643] process > FreebayesSingle (SRR7062655... [ 94%] 697 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3309) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [42/a9e42b] process > HaplotypeCaller (SRR7062655... [ 85%] 627 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 627 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [60/bd3404] process > FreebayesSingle (SRR7062655... [ 94%] 698 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3309) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [f5/8cd562] process > HaplotypeCaller (SRR7062655... [ 85%] 628 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 628 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [60/bd3404] process > FreebayesSingle (SRR7062655... [ 94%] 698 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3311) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [f5/8cd562] process > HaplotypeCaller (SRR7062655... [ 85%] 628 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 628 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [ef/ebb939] process > FreebayesSingle (SRR7062655... [ 94%] 699 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3312) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [09/745387] process > HaplotypeCaller (SRR7062655... [ 85%] 629 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 629 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [15/71b884] process > FreebayesSingle (SRR7062655... [ 95%] 701 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3314) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [09/745387] process > HaplotypeCaller (SRR7062655... [ 85%] 629 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 629 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [1c/c84db7] process > FreebayesSingle (SRR7062655... [ 95%] 701 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3315) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [b5/503346] process > HaplotypeCaller (SRR7062655... [ 85%] 630 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 630 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [d8/510654] process > FreebayesSingle (SRR7062655... [ 95%] 701 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3316) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [1e/4d3f62] process > HaplotypeCaller (SRR7062655... [ 85%] 632 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 632 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [d8/510654] process > FreebayesSingle (SRR7062655... [ 95%] 701 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3317) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [1e/4d3f62] process > HaplotypeCaller (SRR7062655... [ 85%] 632 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 632 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [04/3af256] process > FreebayesSingle (SRR7062655... [ 95%] 701 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3318) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [61/d26d61] process > HaplotypeCaller (SRR7062655... [ 86%] 637 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 637 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [04/3af256] process > FreebayesSingle (SRR7062655... [ 95%] 701 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3322) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [79/1d928b] process > HaplotypeCaller (SRR7062655... [ 86%] 637 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 637 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f0/78dbd2] process > FreebayesSingle (SRR7062655... [ 95%] 701 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3324) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [0e/ea65eb] process > HaplotypeCaller (SRR7062655... [ 86%] 639 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 639 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [d3/214e8d] process > FreebayesSingle (SRR7062655... [ 95%] 702 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3325) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [6f/af4c5d] process > HaplotypeCaller (SRR7062655... [ 86%] 639 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 639 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [d3/214e8d] process > FreebayesSingle (SRR7062655... [ 95%] 702 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3327) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [78/051bcf] process > HaplotypeCaller (SRR7062655... [ 87%] 641 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 641 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [04/3af256] process > FreebayesSingle (SRR7062655... [ 96%] 709 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3333) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [78/051bcf] process > HaplotypeCaller (SRR7062655... [ 87%] 641 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 641 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f3/843e5a] process > FreebayesSingle (SRR7062655... [ 96%] 709 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3334) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [78/051bcf] process > HaplotypeCaller (SRR7062655... [ 87%] 641 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 641 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f0/003d6f] process > FreebayesSingle (SRR7062655... [ 96%] 709 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3336) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [c0/25e6db] process > HaplotypeCaller (SRR7062655... [ 87%] 642 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 642 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [97/86d89d] process > FreebayesSingle (SRR7062655... [ 96%] 710 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3337) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [c0/25e6db] process > HaplotypeCaller (SRR7062655... [ 87%] 642 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 642 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [20/7fef69] process > FreebayesSingle (SRR7062655... [ 96%] 711 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3338) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [7d/83ab7e] process > HaplotypeCaller (SRR7062655... [ 87%] 643 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 643 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [93/582ab8] process > FreebayesSingle (SRR7062655... [ 96%] 711 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3339) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [42/a9e42b] process > HaplotypeCaller (SRR7062655... [ 87%] 646 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 646 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b7/14f7bd] process > FreebayesSingle (SRR7062655... [ 96%] 714 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3344) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [5d/4479cb] process > HaplotypeCaller (SRR7062655... [ 87%] 646 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 646 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [61/47b03a] process > FreebayesSingle (SRR7062655... [ 96%] 714 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/94c681] process > Mpileup (SRR7062655-6_1-354... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3348) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [7d/72337c] process > HaplotypeCaller (SRR7062655... [ 87%] 647 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 647 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [20/7fef69] process > FreebayesSingle (SRR7062655... [ 98%] 723 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c9/7732de] process > Mpileup (SRR7062655-28_1-49... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3353) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [6b/ba3361] process > HaplotypeCaller (SRR7062655... [ 87%] 647 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 647 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [41/916561] process > FreebayesSingle (SRR7062655... [ 98%] 723 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fd/3e305b] process > Mpileup (SRR7062655-W_1-516... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3354) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [6b/ba3361] process > HaplotypeCaller (SRR7062655... [ 87%] 647 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 647 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [41/916561] process > FreebayesSingle (SRR7062655... [ 98%] 723 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1b/ca711f] process > Mpileup (SRR7062655-24_1-62... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3357) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [a6/d21c8e] process > HaplotypeCaller (SRR7062655... [ 88%] 648 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 648 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f0/c197f5] process > FreebayesSingle (SRR7062655... [ 98%] 725 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [03/28ad97] process > Mpileup (SRR7062655-AADN040... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3358) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [79/1d928b] process > HaplotypeCaller (SRR7062655... [ 88%] 649 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 649 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f0/c197f5] process > FreebayesSingle (SRR7062655... [ 98%] 725 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [06/b626cf] process > Mpileup (SRR7062655-AADN040... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3358) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [79/1d928b] process > HaplotypeCaller (SRR7062655... [ 88%] 649 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 649 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f0/c197f5] process > FreebayesSingle (SRR7062655... [ 98%] 725 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [06/b626cf] process > Mpileup (SRR7062655-AADN040... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3359) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [6f/af4c5d] process > HaplotypeCaller (SRR7062655... [ 88%] 650 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 650 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [f0/c197f5] process > FreebayesSingle (SRR7062655... [ 98%] 725 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [dc/33081c] process > Mpileup (SRR7062655-AADN040... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3359) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [6f/af4c5d] process > HaplotypeCaller (SRR7062655... [ 88%] 650 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 650 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [61/47b03a] process > FreebayesSingle (SRR7062655... [ 98%] 726 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [dc/33081c] process > Mpileup (SRR7062655-AADN040... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3360) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [6f/af4c5d] process > HaplotypeCaller (SRR7062655... [ 88%] 650 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 650 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [61/47b03a] process > FreebayesSingle (SRR7062655... [ 98%] 726 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8b/fa2cb3] process > Mpileup (SRR7062655-AADN040... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3361) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [78/051bcf] process > HaplotypeCaller (SRR7062655... [ 88%] 652 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 652 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [b7/14f7bd] process > FreebayesSingle (SRR7062655... [ 98%] 728 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8b/fa2cb3] process > Mpileup (SRR7062655-AADN040... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3367) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [78/051bcf] process > HaplotypeCaller (SRR7062655... [ 88%] 652 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 652 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [3b/bfb04f] process > FreebayesSingle (SRR7062655... [ 99%] 731 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [4c/4a2b61] process > Mpileup (SRR7062655-AADN040... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3368) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [78/051bcf] process > HaplotypeCaller (SRR7062655... [ 88%] 652 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 652 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [41/916561] process > FreebayesSingle (SRR7062655... [ 99%] 732 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1d/9d4108] process > Mpileup (SRR7062655-AADN040... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3369) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [78/051bcf] process > HaplotypeCaller (SRR7062655... [ 88%] 652 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 652 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [76/56f5f8] process > FreebayesSingle (SRR7062655... [ 99%] 734 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6f/022151] process > Mpileup (SRR7062655-AADN040... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3370) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [78/051bcf] process > HaplotypeCaller (SRR7062655... [ 88%] 652 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 652 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [76/56f5f8] process > FreebayesSingle (SRR7062655... [ 99%] 734 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [00/d29bd2] process > Mpileup (SRR7062655-AADN040... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3371) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [34/1e8c94] process > HaplotypeCaller (SRR7062655... [ 88%] 654 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 654 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [76/56f5f8] process > FreebayesSingle (SRR7062655... [ 99%] 734 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [61/1d4f29] process > Mpileup (SRR7062655-AADN040... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3372) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [34/1e8c94] process > HaplotypeCaller (SRR7062655... [ 88%] 654 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 654 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [76/56f5f8] process > FreebayesSingle (SRR7062655... [ 99%] 734 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c7/b89e9a] process > Mpileup (SRR7062655-AADN040... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3373) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [6b/ba3361] process > HaplotypeCaller (SRR7062655... [ 89%] 656 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 656 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [76/56f5f8] process > FreebayesSingle (SRR7062655... [ 99%] 734 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d3/77d972] process > Mpileup (SRR7062655-AADN040... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3374) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [6b/ba3361] process > HaplotypeCaller (SRR7062655... [ 89%] 656 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 656 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [76/56f5f8] process > FreebayesSingle (SRR7062655... [ 99%] 734 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [40/74891c] process > Mpileup (SRR7062655-AADN040... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3376) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [ec/6d7064] process > HaplotypeCaller (SRR7062655... [ 89%] 658 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 658 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5c/ed89be] process > FreebayesSingle (SRR7062655... [ 99%] 735 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6e/8e900a] process > Mpileup (SRR7062655-AADN040... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3377) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [ec/6d7064] process > HaplotypeCaller (SRR7062655... [ 89%] 658 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 658 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5c/ed89be] process > FreebayesSingle (SRR7062655... [ 99%] 735 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1e/0fe028] process > Mpileup (SRR7062655-AADN040... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3378) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [e5/a96080] process > HaplotypeCaller (SRR7062655... [ 89%] 659 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 659 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5c/ed89be] process > FreebayesSingle (SRR7062655... [ 99%] 735 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [32/b43fc7] process > Mpileup (SRR7062655-AADN040... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3380) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5c/ed89be] process > FreebayesSingle (SRR7062655... [ 99%] 735 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2e/7c4a91] process > Mpileup (SRR7062655-AADN040... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3380) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5c/ed89be] process > FreebayesSingle (SRR7062655... [ 99%] 735 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2e/7c4a91] process > Mpileup (SRR7062655-AADN040... [ 52%] 384 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3383) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5c/ed89be] process > FreebayesSingle (SRR7062655... [ 99%] 735 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c5/dca5e9] process > Mpileup (SRR7062655-AADN040... [ 52%] 387 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3385) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5c/ed89be] process > FreebayesSingle (SRR7062655... [ 99%] 735 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d0/c41a52] process > Mpileup (SRR7062655-AADN040... [ 53%] 389 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3386) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5c/ed89be] process > FreebayesSingle (SRR7062655... [ 99%] 735 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [22/466aac] process > Mpileup (SRR7062655-AADN040... [ 53%] 390 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3387) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [5c/ed89be] process > FreebayesSingle (SRR7062655... [ 99%] 735 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [46/2f86ac] process > Mpileup (SRR7062655-AADN040... [ 53%] 391 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3389) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9e/a5424d] process > Mpileup (SRR7062655-AADN040... [ 53%] 392 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3391) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [08/cc4977] process > Mpileup (SRR7062655-AADN040... [ 53%] 394 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3391) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [08/cc4977] process > Mpileup (SRR7062655-AADN040... [ 53%] 394 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3391) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [08/cc4977] process > Mpileup (SRR7062655-AADN040... [ 53%] 394 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3391) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a0/b71f5d] process > Mpileup (SRR7062655-33_1-16... [ 54%] 396 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3394) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [5b/599dd8] process > Mpileup (SRR7062655-AADN040... [ 54%] 397 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3395) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1a/50dcc4] process > Mpileup (SRR7062655-AADN040... [ 54%] 398 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3396) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [91/e963d3] process > Mpileup (SRR7062655-AADN040... [ 54%] 399 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3397) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cb/343fa7] process > Mpileup (SRR7062655-AADN040... [ 54%] 400 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3398) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c2/3534b6] process > Mpileup (SRR7062655-AADN040... [ 54%] 401 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3399) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [42/5b5cfd] process > Mpileup (SRR7062655-AADN040... [ 54%] 402 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3400) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/09656b] process > Mpileup (SRR7062655-AADN040... [ 54%] 403 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3400) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/09656b] process > Mpileup (SRR7062655-AADN040... [ 54%] 403 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3401) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/2cb6c4] process > Mpileup (SRR7062655-AADN040... [ 55%] 404 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3403) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8f/6531e1] process > Mpileup (SRR7062655-AADN040... [ 55%] 406 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3404) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [16/da1d5d] process > Mpileup (SRR7062655-AADN040... [ 55%] 407 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3405) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a6/5ac1c1] process > Mpileup (SRR7062655-AADN040... [ 55%] 408 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3406) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [16/a3cf68] process > Mpileup (SRR7062655-AADN040... [ 55%] 409 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3407) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [de/1e0bbd] process > Mpileup (SRR7062655-AADN040... [ 56%] 411 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3408) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f1/210e15] process > Mpileup (SRR7062655-AADN040... [ 56%] 411 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3409) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [91/1f108d] process > Mpileup (SRR7062655-AADN040... [ 56%] 412 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3410) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [0f/269c84] process > Mpileup (SRR7062655-AADN040... [ 56%] 413 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3411) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ce/ac6025] process > Mpileup (SRR7062655-KQ75957... [ 56%] 414 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3411) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ce/ac6025] process > Mpileup (SRR7062655-KQ75957... [ 56%] 414 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3411) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ce/ac6025] process > Mpileup (SRR7062655-KQ75957... [ 56%] 414 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3411) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [10/02824d] process > Mpileup (SRR7062655-KQ75946... [ 56%] 415 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3413) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [23/60240a] process > Mpileup (SRR7062655-AADN040... [ 56%] 416 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3415) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ef/e2b950] process > Mpileup (SRR7062655-AADN040... [ 56%] 418 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3416) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [72/151c10] process > Mpileup (SRR7062655-AADN040... [ 57%] 419 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3418) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [22/abd54c] process > Mpileup (SRR7062655-KQ75954... [ 57%] 421 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3420) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [20/4cb25a] process > Mpileup (SRR7062655-AADN040... [ 57%] 423 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3421) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [5d/e2ec4e] process > Mpileup (SRR7062655-AADN040... [ 57%] 424 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3422) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cc/c912f1] process > Mpileup (SRR7062655-AADN040... [ 57%] 425 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3423) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [61/32d36d] process > Mpileup (SRR7062655-AADN040... [ 58%] 426 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3423) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [8e/61d8c5] process > HaplotypeCaller (SRR7062655... [ 89%] 661 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 661 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [61/32d36d] process > Mpileup (SRR7062655-AADN040... [ 58%] 426 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3425) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c5/159aa1] process > Mpileup (SRR7062655-AADN040... [ 58%] 427 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3426) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [ 75%] 3 of 4 [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [75/98426f] process > Mpileup (SRR7062655-AADN040... [ 58%] 428 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3426) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [75/98426f] process > Mpileup (SRR7062655-AADN040... [ 58%] 428 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3427) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1b/5952d4] process > Mpileup (SRR7062655-AADN040... [ 58%] 428 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3428) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [05/3ffb11] process > Mpileup (SRR7062655-AADN040... [ 58%] 429 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3428) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [05/3ffb11] process > Mpileup (SRR7062655-AADN040... [ 58%] 429 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3429) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [dc/a8584d] process > Mpileup (SRR7062655-AADN040... [ 58%] 431 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3430) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [90/a2eecb] process > Mpileup (SRR7062655-KQ75962... [ 58%] 431 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3432) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [79/9bee5d] process > Mpileup (SRR7062655-AADN040... [ 59%] 433 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3432) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [91/e963d3] process > Mpileup (SRR7062655-AADN040... [ 59%] 434 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3433) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2e/e2ec44] process > Mpileup (SRR7062655-AADN040... [ 59%] 434 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3433) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [32/b43fc7] process > Mpileup (SRR7062655-AADN040... [ 59%] 435 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3434) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [0c/dd9668] process > Mpileup (SRR7062655-AADN040... [ 59%] 435 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3435) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [3f/8b7982] process > Mpileup (SRR7062655-AADN040... [ 59%] 437 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3436) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d4/08b972] process > Mpileup (SRR7062655-AADN040... [ 59%] 437 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3438) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f4/9d51e0] process > Mpileup (SRR7062655-KQ75948... [ 59%] 439 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3440) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d3/38f04b] process > Mpileup (SRR7062655-AADN040... [ 60%] 441 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3442) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cf/a56997] process > Mpileup (SRR7062655-AADN040... [ 60%] 443 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3443) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f2/7b86d9] process > Mpileup (SRR7062655-AADN040... [ 60%] 444 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3444) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6f/7dcb2f] process > Mpileup (SRR7062655-AADN040... [ 60%] 445 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3447) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [db/e29603] process > Mpileup (SRR7062655-AADN040... [ 61%] 448 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3450) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [76/7581b1] process > Mpileup (SRR7062655-AADN040... [ 61%] 451 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3452) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [55/f80a75] process > Mpileup (SRR7062655-AADN040... [ 61%] 453 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3453) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7d/163b58] process > Mpileup (SRR7062655-AADN040... [ 61%] 454 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3454) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [db/ea1976] process > Mpileup (SRR7062655-AADN040... [ 61%] 455 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3455) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1c/d5e880] process > Mpileup (SRR7062655-KQ75960... [ 62%] 456 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3457) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d3/3bc947] process > Mpileup (SRR7062655-AADN040... [ 62%] 458 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3458) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [88/3f81de] process > Mpileup (SRR7062655-AADN040... [ 62%] 459 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3459) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6b/b55761] process > Mpileup (SRR7062655-AADN040... [ 62%] 460 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3461) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [41/ccf59e] process > Mpileup (SRR7062655-AADN040... [ 62%] 462 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3463) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [50/ed16dd] process > HaplotypeCaller (SRR7062655... [ 89%] 662 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7d/10ca83] process > Mpileup (SRR7062655-AADN040... [ 63%] 464 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3463) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [8a/597c23] process > HaplotypeCaller (SRR7062655... [ 90%] 663 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 662 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7d/10ca83] process > Mpileup (SRR7062655-AADN040... [ 63%] 464 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3465) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [8a/597c23] process > HaplotypeCaller (SRR7062655... [ 90%] 663 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 663 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b0/75ad5b] process > Mpileup (SRR7062655-AADN040... [ 63%] 465 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3467) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [8a/597c23] process > HaplotypeCaller (SRR7062655... [ 90%] 663 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 663 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [59/a720f3] process > Mpileup (SRR7062655-AADN040... [ 63%] 467 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3468) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [8a/597c23] process > HaplotypeCaller (SRR7062655... [ 90%] 663 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 663 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ca/be098b] process > Mpileup (SRR7062655-AADN040... [ 63%] 468 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3470) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [8a/597c23] process > HaplotypeCaller (SRR7062655... [ 90%] 663 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 663 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [e7/b5f557] process > Mpileup (SRR7062655-AADN040... [ 64%] 470 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3471) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [8a/597c23] process > HaplotypeCaller (SRR7062655... [ 90%] 663 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 663 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9b/c95b54] process > Mpileup (SRR7062655-AADN040... [ 64%] 471 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3473) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [8a/597c23] process > HaplotypeCaller (SRR7062655... [ 90%] 663 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 663 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fc/44f41b] process > Mpileup (SRR7062655-AADN040... [ 64%] 473 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3474) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [8a/597c23] process > HaplotypeCaller (SRR7062655... [ 90%] 663 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 663 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [aa/c1f598] process > Mpileup (SRR7062655-AADN040... [ 64%] 474 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3475) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [8a/597c23] process > HaplotypeCaller (SRR7062655... [ 90%] 663 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 663 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b5/dbc53b] process > Mpileup (SRR7062655-AADN040... [ 64%] 475 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3477) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [8a/597c23] process > HaplotypeCaller (SRR7062655... [ 90%] 663 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 663 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [56/21a088] process > Mpileup (SRR7062655-AADN040... [ 64%] 477 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3480) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [8a/597c23] process > HaplotypeCaller (SRR7062655... [ 90%] 663 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 663 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7d/8a8a68] process > Mpileup (SRR7062655-AADN040... [ 65%] 482 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3482) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [8a/597c23] process > HaplotypeCaller (SRR7062655... [ 90%] 663 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 663 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d2/0830f7] process > Mpileup (SRR7062655-AADN040... [ 65%] 482 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3482) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [8a/597c23] process > HaplotypeCaller (SRR7062655... [ 90%] 663 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 663 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d2/0830f7] process > Mpileup (SRR7062655-AADN040... [ 65%] 482 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3483) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [8a/597c23] process > HaplotypeCaller (SRR7062655... [ 90%] 663 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 663 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [0f/57fd09] process > Mpileup (SRR7062655-AADN040... [ 65%] 483 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3484) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [8a/597c23] process > HaplotypeCaller (SRR7062655... [ 90%] 663 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 663 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d2/067bce] process > Mpileup (SRR7062655-AADN040... [ 65%] 484 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3484) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [8a/597c23] process > HaplotypeCaller (SRR7062655... [ 90%] 663 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 663 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d2/067bce] process > Mpileup (SRR7062655-AADN040... [ 65%] 484 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3485) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [8a/597c23] process > HaplotypeCaller (SRR7062655... [ 90%] 663 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 663 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b1/b23daf] process > Mpileup (SRR7062655-AADN040... [ 66%] 485 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3486) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [8a/597c23] process > HaplotypeCaller (SRR7062655... [ 90%] 663 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 663 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b7/f967c7] process > Mpileup (SRR7062655-AADN040... [ 66%] 486 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3489) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [97/b5452c] process > HaplotypeCaller (SRR7062655... [ 90%] 664 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 664 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [5e/a5bbd9] process > Mpileup (SRR7062655-AADN040... [ 66%] 488 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3489) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [97/b5452c] process > HaplotypeCaller (SRR7062655... [ 90%] 664 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 664 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d4/08b972] process > Mpileup (SRR7062655-AADN040... [ 66%] 489 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3490) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [97/b5452c] process > HaplotypeCaller (SRR7062655... [ 90%] 664 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 664 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6e/4b3878] process > Mpileup (SRR7062655-KQ75957... [ 66%] 489 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3491) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [0c/c486da] process > HaplotypeCaller (SRR7062655... [ 90%] 665 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 665 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ea/b11415] process > Mpileup (SRR7062655-AADN040... [ 66%] 490 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3492) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [0c/c486da] process > HaplotypeCaller (SRR7062655... [ 90%] 665 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 665 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [35/873798] process > Mpileup (SRR7062655-AADN040... [ 66%] 490 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3493) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [0c/c486da] process > HaplotypeCaller (SRR7062655... [ 90%] 665 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 665 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [88/993b38] process > Mpileup (SRR7062655-AADN040... [ 66%] 492 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3494) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [0c/c486da] process > HaplotypeCaller (SRR7062655... [ 90%] 665 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 665 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [76/202790] process > Mpileup (SRR7062655-AADN040... [ 66%] 492 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3494) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [0c/c486da] process > HaplotypeCaller (SRR7062655... [ 90%] 665 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 665 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [76/202790] process > Mpileup (SRR7062655-AADN040... [ 66%] 492 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3495) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [0c/c486da] process > HaplotypeCaller (SRR7062655... [ 90%] 665 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 665 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c8/a347f3] process > Mpileup (SRR7062655-AADN040... [ 67%] 493 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3496) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [0c/c486da] process > HaplotypeCaller (SRR7062655... [ 90%] 665 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 665 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [90/f6d2e5] process > Mpileup (SRR7062655-AADN040... [ 67%] 494 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3496) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [0c/c486da] process > HaplotypeCaller (SRR7062655... [ 90%] 665 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 665 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [90/f6d2e5] process > Mpileup (SRR7062655-AADN040... [ 67%] 494 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3497) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [0c/c486da] process > HaplotypeCaller (SRR7062655... [ 90%] 665 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 665 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c8/29ee62] process > Mpileup (SRR7062655-AADN040... [ 67%] 495 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3498) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [0c/c486da] process > HaplotypeCaller (SRR7062655... [ 90%] 665 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 665 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fa/309de4] process > Mpileup (SRR7062655-AADN040... [ 67%] 496 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3499) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [0c/c486da] process > HaplotypeCaller (SRR7062655... [ 90%] 665 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 665 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [5d/20ffff] process > Mpileup (SRR7062655-AADN040... [ 67%] 497 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3500) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [0c/c486da] process > HaplotypeCaller (SRR7062655... [ 90%] 665 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 665 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [93/1665bc] process > Mpileup (SRR7062655-AADN040... [ 67%] 498 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3502) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [0c/c486da] process > HaplotypeCaller (SRR7062655... [ 90%] 665 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 665 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [17/2ba30a] process > Mpileup (SRR7062655-AADN040... [ 68%] 500 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3505) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [0c/c486da] process > HaplotypeCaller (SRR7062655... [ 90%] 665 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 665 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7e/4385e9] process > Mpileup (SRR7062655-AADN040... [ 68%] 503 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3507) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [0c/c486da] process > HaplotypeCaller (SRR7062655... [ 90%] 665 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 665 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f3/13364f] process > Mpileup (SRR7062655-AADN040... [ 68%] 505 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3509) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [0c/c486da] process > HaplotypeCaller (SRR7062655... [ 90%] 665 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 665 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a6/fac6db] process > Mpileup (SRR7062655-AADN040... [ 69%] 507 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3511) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [0c/c486da] process > HaplotypeCaller (SRR7062655... [ 90%] 665 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 665 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [e7/a4da90] process > Mpileup (SRR7062655-AADN040... [ 69%] 509 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3514) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [dc/5a4a09] process > HaplotypeCaller (SRR7062654... [ 90%] 666 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 666 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [e1/c0b9a5] process > Mpileup (SRR7062655-AADN040... [ 69%] 511 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3514) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [dc/5a4a09] process > HaplotypeCaller (SRR7062654... [ 90%] 666 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 666 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c0/53554e] process > Mpileup (SRR7062655-AADN040... [ 69%] 512 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3515) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [dc/5a4a09] process > HaplotypeCaller (SRR7062654... [ 90%] 666 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 666 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [62/9bbe4f] process > Mpileup (SRR7062655-AADN040... [ 69%] 512 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3515) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [dc/5a4a09] process > HaplotypeCaller (SRR7062654... [ 90%] 666 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 666 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [62/9bbe4f] process > Mpileup (SRR7062655-AADN040... [ 69%] 512 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3515) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [dc/5a4a09] process > HaplotypeCaller (SRR7062654... [ 90%] 666 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 666 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [62/9bbe4f] process > Mpileup (SRR7062655-AADN040... [ 69%] 512 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3516) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [dc/5a4a09] process > HaplotypeCaller (SRR7062654... [ 90%] 666 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 666 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [43/db3ce0] process > Mpileup (SRR7062655-AADN040... [ 69%] 513 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3517) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [dc/5a4a09] process > HaplotypeCaller (SRR7062654... [ 90%] 666 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 666 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [cb/9556d5] process > Mpileup (SRR7062655-AADN040... [ 70%] 516 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3520) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [dc/5a4a09] process > HaplotypeCaller (SRR7062654... [ 90%] 666 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 666 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [bc/8ad4ad] process > Mpileup (SRR7062655-AADN040... [ 70%] 517 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3520) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [dc/5a4a09] process > HaplotypeCaller (SRR7062654... [ 90%] 666 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 666 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [0f/5871c4] process > FreebayesSingle (SRR7062654... [ 99%] 736 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [bc/8ad4ad] process > Mpileup (SRR7062655-AADN040... [ 70%] 517 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3521) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [dc/5a4a09] process > HaplotypeCaller (SRR7062654... [ 90%] 666 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 666 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [06/490bf8] process > FreebayesSingle (SRR7062655... [100%] 737 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [3f/38fb79] process > Mpileup (SRR7062655-AADN040... [ 70%] 517 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3522) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [dc/5a4a09] process > HaplotypeCaller (SRR7062654... [ 90%] 666 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 666 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [06/490bf8] process > FreebayesSingle (SRR7062655... [100%] 737 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [59/1d25ee] process > Mpileup (SRR7062655-AADN040... [ 70%] 518 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3523) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [dc/5a4a09] process > HaplotypeCaller (SRR7062654... [ 90%] 666 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 666 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [06/490bf8] process > FreebayesSingle (SRR7062655... [100%] 737 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6c/9e9a8b] process > Mpileup (SRR7062655-AADN040... [ 70%] 519 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3525) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [06/490bf8] process > FreebayesSingle (SRR7062655... [100%] 737 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [46/3d8ebc] process > Mpileup (SRR7062655-AADN040... [ 70%] 521 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3526) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [06/490bf8] process > FreebayesSingle (SRR7062655... [100%] 737 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [63/5893d6] process > Mpileup (SRR7062655-AADN040... [ 70%] 521 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3528) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d0/21b8a5] process > Mpileup (SRR7062655-AADN040... [ 71%] 522 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3529) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [24/2b3c6c] process > Mpileup (SRR7062655-AADN040... [ 71%] 523 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3531) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [db/19c894] process > Mpileup (SRR7062655-KQ75967... [ 71%] 525 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3533) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a4/0fd0a9] process > Mpileup (SRR7062655-AADN040... [ 71%] 527 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3533) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a4/0fd0a9] process > Mpileup (SRR7062655-AADN040... [ 71%] 527 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3536) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [20/5c7de5] process > Mpileup (SRR7062655-AADN040... [ 72%] 530 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3536) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [20/5c7de5] process > Mpileup (SRR7062655-AADN040... [ 72%] 530 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3539) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d4/ba58de] process > Mpileup (SRR7062655-AADN040... [ 72%] 533 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3540) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [11/290ef2] process > Mpileup (SRR7062655-AADN040... [ 72%] 534 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3541) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [5f/33762b] process > Mpileup (SRR7062655-AADN040... [ 72%] 535 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3542) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [25/229ac9] process > Mpileup (SRR7062655-AADN040... [ 72%] 536 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3542) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [88/993b38] process > Mpileup (SRR7062655-AADN040... [ 73%] 537 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3543) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [0b/232a86] process > Mpileup (SRR7062655-AADN040... [ 73%] 537 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3543) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [80/f756fa] process > Mpileup (SRR7062655-AADN040... [ 73%] 538 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3544) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c9/450f6d] process > Mpileup (SRR7062655-AADN040... [ 73%] 538 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3545) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [af/5a6cd5] process > Mpileup (SRR7062655-AADN040... [ 73%] 540 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3546) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [99/e2f084] process > Mpileup (SRR7062655-AADN040... [ 73%] 540 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3547) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7b/b74980] process > Mpileup (SRR7062655-AADN040... [ 73%] 541 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3547) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7b/b74980] process > Mpileup (SRR7062655-AADN040... [ 73%] 541 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3548) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f8/52e0f8] process > Mpileup (SRR7062655-AADN040... [ 73%] 542 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3549) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [26/9417d5] process > Mpileup (SRR7062655-AADN040... [ 73%] 543 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3550) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7f/fb876b] process > Mpileup (SRR7062655-AADN040... [ 74%] 544 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3550) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7f/fb876b] process > Mpileup (SRR7062655-AADN040... [ 74%] 544 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3551) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9c/1a351c] process > Mpileup (SRR7062655-AADN040... [ 74%] 545 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3553) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [da/e219dd] process > Mpileup (SRR7062655-AADN040... [ 74%] 547 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3556) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [08/f6bcc3] process > Mpileup (SRR7062655-AADN040... [ 74%] 550 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3557) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ba/871725] process > Mpileup (SRR7062655-AADN040... [ 74%] 551 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3559) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ba/4c32cd] process > Mpileup (SRR7062655-AADN040... [ 75%] 553 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3559) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ba/4c32cd] process > Mpileup (SRR7062655-AADN040... [ 75%] 553 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3560) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c2/5315e8] process > Mpileup (SRR7062655-AADN040... [ 75%] 554 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3561) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [df/38ab62] process > Mpileup (SRR7062655-AADN040... [ 75%] 555 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3565) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8c/96ca32] process > Mpileup (SRR7062655-AADN040... [ 76%] 559 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3566) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f6/8b0234] process > Mpileup (SRR7062655-AADN040... [ 76%] 560 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3567) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [18/d1cd13] process > Mpileup (SRR7062655-AADN040... [ 76%] 561 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3569) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2c/e7a8af] process > Mpileup (SRR7062655-AADN040... [ 76%] 563 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3569) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [43/db3ce0] process > Mpileup (SRR7062655-AADN040... [ 76%] 564 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3570) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [5a/588607] process > Mpileup (SRR7062655-AADN040... [ 76%] 564 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3570) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fd/a69dc1] process > Mpileup (SRR7062655-AADN040... [ 76%] 565 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3571) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [e6/c76ea0] process > Mpileup (SRR7062655-AADN040... [ 76%] 565 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3572) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b4/33063a] process > Mpileup (SRR7062655-AADN040... [ 76%] 566 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3573) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9d/906714] process > Mpileup (SRR7062655-AADN040... [ 77%] 567 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3574) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [09/55b2d3] process > Mpileup (SRR7062655-AADN040... [ 77%] 569 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3575) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1f/0a4b68] process > Mpileup (SRR7062655-AADN040... [ 77%] 569 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3576) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f2/04aa06] process > Mpileup (SRR7062655-AADN040... [ 77%] 572 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3578) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [90/36e7f1] process > Mpileup (SRR7062655-AADN040... [ 77%] 572 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3579) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [56/12104e] process > Mpileup (SRR7062655-AADN040... [ 77%] 573 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3580) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [e3/62ebce] process > Mpileup (SRR7062655-AADN040... [ 78%] 574 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3581) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fe/45452b] process > Mpileup (SRR7062655-AADN040... [ 78%] 575 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3582) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [55/2c6e60] process > Mpileup (SRR7062655-AADN040... [ 78%] 576 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3582) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [55/2c6e60] process > Mpileup (SRR7062655-AADN040... [ 78%] 576 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3583) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fd/7cd2a5] process > Mpileup (SRR7062655-AADN040... [ 78%] 577 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3584) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [50/f63a60] process > Mpileup (SRR7062655-AADN040... [ 78%] 578 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3584) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [50/f63a60] process > Mpileup (SRR7062655-AADN040... [ 78%] 578 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3587) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f3/f0916d] process > Mpileup (SRR7062655-AADN040... [ 79%] 581 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3589) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2b/ad3969] process > Mpileup (SRR7062655-AADN040... [ 79%] 583 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3590) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [4c/c399dc] process > Mpileup (SRR7062655-AADN040... [ 79%] 584 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3591) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/1bce8f] process > Mpileup (SRR7062655-AADN040... [ 79%] 585 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3593) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c8/dc0af1] process > Mpileup (SRR7062655-AADN040... [ 79%] 587 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3594) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [92/d1755d] process > Mpileup (SRR7062655-AADN040... [ 79%] 588 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3595) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ee/25a68a] process > Mpileup (SRR7062655-AADN040... [ 80%] 589 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3595) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [20/5c7de5] process > Mpileup (SRR7062655-AADN040... [ 80%] 591 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3597) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f0/f31165] process > Mpileup (SRR7062655-AADN040... [ 80%] 591 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3597) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [99/e2f084] process > Mpileup (SRR7062655-AADN040... [ 80%] 593 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3599) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8e/9c9fe5] process > Mpileup (SRR7062655-AADN040... [ 80%] 593 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3600) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [75/cb6760] process > Mpileup (SRR7062655-AADN040... [ 80%] 594 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3601) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [5e/825360] process > Mpileup (SRR7062655-AADN040... [ 81%] 596 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3602) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [4f/61b834] process > Mpileup (SRR7062655-AADN040... [ 81%] 596 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3603) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [5e/01be07] process > Mpileup (SRR7062655-AADN040... [ 81%] 597 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3605) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c1/a00e2a] process > Mpileup (SRR7062655-AADN040... [ 81%] 599 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3606) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [46/28f039] process > Mpileup (SRR7062655-AADN040... [ 81%] 600 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3608) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b2/88253a] process > Mpileup (SRR7062655-AADN040... [ 81%] 602 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3609) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [74/ccd501] process > Mpileup (SRR7062655-AADN040... [ 81%] 603 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3611) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b2/1dbe67] process > Mpileup (SRR7062655-AADN040... [ 82%] 605 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3612) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d1/8c8012] process > Mpileup (SRR7062655-AADN040... [ 82%] 610 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3616) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c4/149ade] process > Mpileup (SRR7062655-AADN040... [ 82%] 610 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3616) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c4/149ade] process > Mpileup (SRR7062655-AADN040... [ 82%] 610 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3617) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b8/90ab49] process > Mpileup (SRR7062655-AADN040... [ 83%] 611 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3618) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6c/529379] process > Mpileup (SRR7062655-AADN040... [ 83%] 612 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3620) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8a/b7ef41] process > Mpileup (SRR7062655-AADN040... [ 83%] 614 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3622) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f5/58de65] process > Mpileup (SRR7062655-AADN040... [ 83%] 616 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3623) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [80/d2ca77] process > Mpileup (SRR7062655-AADN040... [ 83%] 617 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3624) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [83/8816e0] process > Mpileup (SRR7062655-AADN040... [ 84%] 618 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3624) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8a/f6d0d3] process > Mpileup (SRR7062655-AADN040... [ 84%] 619 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3626) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [70/ee3ab1] process > Mpileup (SRR7062655-AADN040... [ 84%] 620 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3626) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [70/ee3ab1] process > Mpileup (SRR7062655-AADN040... [ 84%] 620 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3626) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [70/ee3ab1] process > Mpileup (SRR7062655-AADN040... [ 84%] 620 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3626) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f0/60d8f2] process > Mpileup (SRR7062655-AADN040... [ 84%] 622 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3628) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2d/7fb28d] process > Mpileup (SRR7062655-AADN040... [ 84%] 622 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3629) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [e1/f50523] process > Mpileup (SRR7062655-AADN040... [ 84%] 624 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3630) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [38/4fe36c] process > Mpileup (SRR7062655-AADN040... [ 84%] 624 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3632) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [98/fcf45b] process > Mpileup (SRR7062655-AADN040... [ 85%] 626 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3634) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [e4/0881a0] process > Mpileup (SRR7062655-AADN040... [ 85%] 628 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3635) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [18/ba9e73] process > Mpileup (SRR7062655-AADN040... [ 85%] 629 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3637) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/ff30c5] process > HaplotypeCaller (SRR7062654... [ 90%] 667 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 667 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [94/0f4868] process > Mpileup (SRR7062655-AADN040... [ 85%] 631 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3639) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [12/8cda67] process > HaplotypeCaller (SRR7062654... [ 90%] 668 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 668 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [bf/5afd3e] process > Mpileup (SRR7062655-AADN040... [ 85%] 632 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3639) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [12/8cda67] process > HaplotypeCaller (SRR7062654... [ 90%] 668 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 668 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [4e/2d71c3] process > Mpileup (SRR7062655-AADN040... [ 85%] 632 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3640) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [2c/4a8ace] process > HaplotypeCaller (SRR7062655... [ 90%] 669 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 669 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [36/a6e81e] process > Mpileup (SRR7062655-AADN040... [ 85%] 632 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3641) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [2c/4a8ace] process > HaplotypeCaller (SRR7062655... [ 90%] 669 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 669 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c0/62cea3] process > Mpileup (SRR7062655-AADN040... [ 86%] 633 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3642) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [2c/4a8ace] process > HaplotypeCaller (SRR7062655... [ 90%] 669 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 669 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [dd/4c3032] process > Mpileup (SRR7062655-AADN040... [ 86%] 634 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3644) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [2c/4a8ace] process > HaplotypeCaller (SRR7062655... [ 90%] 669 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 669 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [94/1c8edf] process > Mpileup (SRR7062655-AADN040... [ 86%] 636 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3645) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [2c/4a8ace] process > HaplotypeCaller (SRR7062655... [ 90%] 669 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 669 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8f/be64b8] process > Mpileup (SRR7062655-AADN040... [ 86%] 637 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3646) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [2c/4a8ace] process > HaplotypeCaller (SRR7062655... [ 90%] 669 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 669 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a2/53f017] process > Mpileup (SRR7062655-AADN040... [ 86%] 638 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3647) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [2c/4a8ace] process > HaplotypeCaller (SRR7062655... [ 90%] 669 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 669 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [74/b7820f] process > Mpileup (SRR7062655-AADN040... [ 86%] 639 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3648) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [2c/4a8ace] process > HaplotypeCaller (SRR7062655... [ 90%] 669 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 669 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f2/774592] process > Mpileup (SRR7062655-AADN040... [ 86%] 640 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3649) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [2c/4a8ace] process > HaplotypeCaller (SRR7062655... [ 90%] 669 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 669 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d8/288e84] process > Mpileup (SRR7062655-AADN040... [ 87%] 641 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3653) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e7/2e5c73] process > HaplotypeCaller (SRR7062655... [ 91%] 670 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 670 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6d/21de32] process > Mpileup (SRR7062655-AADN040... [ 87%] 644 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3654) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e7/2e5c73] process > HaplotypeCaller (SRR7062655... [ 91%] 670 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 670 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [4c/d31e58] process > FreebayesSingle (SRR7062655... [100%] 738 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [45/2dc230] process > Mpileup (SRR7062655-AADN040... [ 87%] 645 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3654) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e7/2e5c73] process > HaplotypeCaller (SRR7062655... [ 91%] 670 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 670 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [e6/c76ea0] process > Mpileup (SRR7062655-AADN040... [ 87%] 646 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3657) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e7/2e5c73] process > HaplotypeCaller (SRR7062655... [ 91%] 670 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 670 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [09/edbaa3] process > Mpileup (SRR7062655-AADN040... [ 87%] 647 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3657) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e7/2e5c73] process > HaplotypeCaller (SRR7062655... [ 91%] 670 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 670 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1f/0a4b68] process > Mpileup (SRR7062655-AADN040... [ 88%] 649 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3659) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e7/2e5c73] process > HaplotypeCaller (SRR7062655... [ 91%] 670 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 670 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d2/45bfc2] process > Mpileup (SRR7062655-AADN040... [ 88%] 649 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3660) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e7/2e5c73] process > HaplotypeCaller (SRR7062655... [ 91%] 670 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 670 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [63/8e5519] process > Mpileup (SRR7062655-AADN040... [ 88%] 650 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3660) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e7/2e5c73] process > HaplotypeCaller (SRR7062655... [ 91%] 670 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 670 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [63/8e5519] process > Mpileup (SRR7062655-AADN040... [ 88%] 650 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3661) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e7/2e5c73] process > HaplotypeCaller (SRR7062655... [ 91%] 670 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 670 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b5/0a72e1] process > Mpileup (SRR7062655-AADN040... [ 88%] 651 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3662) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e7/2e5c73] process > HaplotypeCaller (SRR7062655... [ 91%] 670 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 670 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [12/4672f9] process > Mpileup (SRR7062655-AADN040... [ 88%] 652 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3663) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e7/2e5c73] process > HaplotypeCaller (SRR7062655... [ 91%] 670 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 670 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [db/f5837a] process > Mpileup (SRR7062655-AADN040... [ 88%] 653 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3663) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e7/2e5c73] process > HaplotypeCaller (SRR7062655... [ 91%] 670 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 670 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [db/f5837a] process > Mpileup (SRR7062655-AADN040... [ 88%] 653 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3664) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e7/2e5c73] process > HaplotypeCaller (SRR7062655... [ 91%] 670 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 670 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b2/c0b067] process > Mpileup (SRR7062655-AADN040... [ 88%] 654 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3666) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e7/2e5c73] process > HaplotypeCaller (SRR7062655... [ 91%] 670 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 670 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c1/76c839] process > Mpileup (SRR7062655-AADN040... [ 89%] 656 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3667) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e7/2e5c73] process > HaplotypeCaller (SRR7062655... [ 91%] 670 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 670 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [46/584e29] process > Mpileup (SRR7062655-AADN040... [ 89%] 657 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3668) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [0d/b26611] process > HaplotypeCaller (SRR7062655... [ 91%] 671 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 671 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [46/584e29] process > Mpileup (SRR7062655-AADN040... [ 89%] 657 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3670) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [48/b93d28] process > HaplotypeCaller (SRR7062655... [ 91%] 671 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 671 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ba/c6b947] process > Mpileup (SRR7062655-AADN040... [ 89%] 659 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3671) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [48/b93d28] process > HaplotypeCaller (SRR7062655... [ 91%] 671 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 671 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b3/b35330] process > Mpileup (SRR7062655-AADN040... [ 89%] 660 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3674) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [82/df8c41] process > HaplotypeCaller (SRR7062655... [ 91%] 671 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 671 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [93/d09ccd] process > Mpileup (SRR7062655-AADN040... [ 90%] 663 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3675) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [18/36fd19] process > HaplotypeCaller (SRR7062655... [ 91%] 671 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 671 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d1/8c8012] process > Mpileup (SRR7062655-AADN040... [ 90%] 664 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3676) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/dc9427] process > HaplotypeCaller (SRR7062655... [ 91%] 671 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 671 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8a/b7ef41] process > Mpileup (SRR7062655-AADN040... [ 90%] 665 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3677) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e8/e67568] process > HaplotypeCaller (SRR7062655... [ 91%] 671 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 671 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [58/9b3926] process > Mpileup (SRR7062655-AADN040... [ 90%] 666 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3679) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b6/a09984] process > HaplotypeCaller (SRR7062655... [ 91%] 671 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 671 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c1/a00e2a] process > Mpileup (SRR7062655-AADN040... [ 90%] 668 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3682) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [2d/f2092b] process > HaplotypeCaller (SRR7062655... [ 91%] 671 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 671 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [70/ee3ab1] process > Mpileup (SRR7062655-AADN040... [ 91%] 671 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3683) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [ec/0c6c93] process > HaplotypeCaller (SRR7062655... [ 91%] 671 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 671 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6c/529379] process > Mpileup (SRR7062655-AADN040... [ 91%] 672 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3684) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [95/68b96b] process > HaplotypeCaller (SRR7062655... [ 91%] 671 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 671 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [41/5a6a6d] process > Mpileup (SRR7062655-AADN040... [ 91%] 673 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3684) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [95/68b96b] process > HaplotypeCaller (SRR7062655... [ 91%] 671 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 671 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2b/ad3969] process > Mpileup (SRR7062655-AADN040... [ 91%] 674 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3687) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [97/969302] process > HaplotypeCaller (SRR7062655... [ 91%] 673 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 673 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2b/ad3969] process > Mpileup (SRR7062655-AADN040... [ 91%] 674 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3687) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [82/df8c41] process > HaplotypeCaller (SRR7062655... [ 91%] 674 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 674 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2b/ad3969] process > Mpileup (SRR7062655-AADN040... [ 91%] 674 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3688) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [2e/788db9] process > HaplotypeCaller (SRR7062655... [ 91%] 674 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 674 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [2b/ad3969] process > Mpileup (SRR7062655-AADN040... [ 91%] 674 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3689) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b0/dd979d] process > HaplotypeCaller (SRR7062655... [ 91%] 674 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 674 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ee/25a68a] process > Mpileup (SRR7062655-AADN040... [ 91%] 675 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3690) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [2d/3351ad] process > HaplotypeCaller (SRR7062655... [ 91%] 677 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 677 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [05/f7c471] process > Mpileup (SRR7062655-AADN040... [ 91%] 677 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3694) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e4/189903] process > HaplotypeCaller (SRR7062655... [ 91%] 677 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 677 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [05/f7c471] process > Mpileup (SRR7062655-AADN040... [ 91%] 677 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3695) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/86099a] process > HaplotypeCaller (SRR7062655... [ 92%] 678 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 678 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [e1/f50523] process > Mpileup (SRR7062655-AADN040... [ 92%] 678 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3696) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [5c/f976db] process > HaplotypeCaller (SRR7062655... [ 92%] 678 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 678 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [e1/f50523] process > Mpileup (SRR7062655-AADN040... [ 92%] 678 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3698) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [00/fdc5e0] process > HaplotypeCaller (SRR7062655... [ 92%] 680 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 680 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c8/dc0af1] process > Mpileup (SRR7062655-AADN040... [ 92%] 679 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3699) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [7b/79147d] process > HaplotypeCaller (SRR7062655... [ 92%] 680 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 680 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c8/dc0af1] process > Mpileup (SRR7062655-AADN040... [ 92%] 679 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3701) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [0c/ef69c9] process > HaplotypeCaller (SRR7062655... [ 92%] 681 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 681 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d6/c4fd1b] process > Mpileup (SRR7062655-AADN040... [ 92%] 680 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3702) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [59/974e7e] process > HaplotypeCaller (SRR7062655... [ 92%] 681 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 681 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8e/9c9fe5] process > Mpileup (SRR7062655-AADN040... [ 92%] 681 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3704) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [ee/99b0b4] process > HaplotypeCaller (SRR7062655... [ 92%] 682 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 682 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [1d/7e5650] process > Mpileup (SRR7062655-AADN040... [ 92%] 682 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3707) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [76/f19ab2] process > HaplotypeCaller (SRR7062655... [ 93%] 685 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 685 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [5e/825360] process > Mpileup (SRR7062655-AADN040... [ 92%] 683 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3708) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [79/dfdee5] process > HaplotypeCaller (SRR7062655... [ 93%] 685 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 685 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [5e/825360] process > Mpileup (SRR7062655-AADN040... [ 92%] 683 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3711) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [25/9ef7f8] process > HaplotypeCaller (SRR7062655... [ 93%] 687 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 687 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [75/cb6760] process > Mpileup (SRR7062655-AADN040... [ 92%] 684 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3714) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [ce/bbfd2c] process > HaplotypeCaller (SRR7062655... [ 93%] 689 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 689 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ad/12fc23] process > Mpileup (SRR7062655-AADN040... [ 93%] 685 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3716) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [52/569d3d] process > HaplotypeCaller (SRR7062655... [ 93%] 691 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 691 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ad/12fc23] process > Mpileup (SRR7062655-AADN040... [ 93%] 685 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3718) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 94%] 692 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 692 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [94/0f4868] process > Mpileup (SRR7062655-AADN040... [ 93%] 686 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3721) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [4e/ec35ad] process > HaplotypeCaller (SRR7062655... [ 94%] 694 of 740 [- ] process > GenotypeGVCFs [ 0%] 0 of 694 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [ 93%] 687 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3724) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [79/dfdee5] process > HaplotypeCaller (SRR7062655... [ 94%] 698 of 740 [5f/e4d50b] process > GenotypeGVCFs (SRR7062654-W... [ 0%] 0 of 698 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [ 93%] 687 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3725) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [79/dfdee5] process > HaplotypeCaller (SRR7062655... [ 94%] 698 of 740 [56/47ac4a] process > GenotypeGVCFs (SRR7062654-A... [ 0%] 0 of 698 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [ 93%] 687 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3725) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [79/dfdee5] process > HaplotypeCaller (SRR7062655... [ 94%] 698 of 740 [56/47ac4a] process > GenotypeGVCFs (SRR7062654-A... [ 0%] 0 of 698 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f0/f31165] process > Mpileup (SRR7062655-AADN040... [ 93%] 688 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3728) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [00/fdc5e0] process > HaplotypeCaller (SRR7062655... [ 94%] 699 of 740 [d3/d6a2f3] process > GenotypeGVCFs (SRR7062654-A... [ 0%] 0 of 699 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [50/8ed802] process > Mpileup (SRR7062655-AADN040... [ 93%] 689 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3729) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [4c/66109c] process > HaplotypeCaller (SRR7062655... [ 95%] 700 of 740 [bd/ab9e13] process > GenotypeGVCFs (SRR7062654-A... [ 0%] 0 of 700 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [50/8ed802] process > Mpileup (SRR7062655-AADN040... [ 93%] 689 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3730) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/86099a] process > HaplotypeCaller (SRR7062655... [ 95%] 702 of 740 [23/2ef233] process > GenotypeGVCFs (SRR7062654-A... [ 0%] 0 of 702 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [50/8ed802] process > Mpileup (SRR7062655-AADN040... [ 93%] 689 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3731) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f3/86099a] process > HaplotypeCaller (SRR7062655... [ 95%] 702 of 740 [a2/407f60] process > GenotypeGVCFs (SRR7062654-A... [ 0%] 0 of 702 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [50/8ed802] process > Mpileup (SRR7062655-AADN040... [ 93%] 689 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3732) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [4a/0979e7] process > HaplotypeCaller (SRR7062655... [ 95%] 703 of 740 [f9/463a0d] process > GenotypeGVCFs (SRR7062654-A... [ 0%] 0 of 703 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [50/8ed802] process > Mpileup (SRR7062655-AADN040... [ 93%] 689 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3733) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [cb/be2d07] process > HaplotypeCaller (SRR7062655... [ 96%] 707 of 740 [74/5f918c] process > GenotypeGVCFs (SRR7062654-A... [ 0%] 0 of 707 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [50/8ed802] process > Mpileup (SRR7062655-AADN040... [ 93%] 689 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3736) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [cb/be2d07] process > HaplotypeCaller (SRR7062655... [ 96%] 707 of 740 [57/f71925] process > GenotypeGVCFs (SRR7062654-K... [ 0%] 0 of 707 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [50/8ed802] process > Mpileup (SRR7062655-AADN040... [ 93%] 689 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3737) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [cb/428af6] process > HaplotypeCaller (SRR7062655... [ 96%] 708 of 740 [79/81bd93] process > GenotypeGVCFs (SRR7062654-A... [ 0%] 0 of 708 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [50/8ed802] process > Mpileup (SRR7062655-AADN040... [ 93%] 689 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3737) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [cb/428af6] process > HaplotypeCaller (SRR7062655... [ 96%] 708 of 740 [79/81bd93] process > GenotypeGVCFs (SRR7062654-A... [ 0%] 0 of 708 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [50/8ed802] process > Mpileup (SRR7062655-AADN040... [ 93%] 689 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3739) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [31/283834] process > HaplotypeCaller (SRR7062655... [ 96%] 710 of 740 [4f/00714d] process > GenotypeGVCFs (SRR7062654-A... [ 0%] 0 of 710 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d8/da3b85] process > Mpileup (SRR7062655-AADN040... [ 93%] 690 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3740) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [31/283834] process > HaplotypeCaller (SRR7062655... [ 96%] 710 of 740 [88/1e291b] process > GenotypeGVCFs (SRR7062654-A... [ 0%] 0 of 710 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d8/da3b85] process > Mpileup (SRR7062655-AADN040... [ 93%] 690 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3742) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [4e/ec35ad] process > HaplotypeCaller (SRR7062655... [ 97%] 715 of 740 [6a/909aa3] process > GenotypeGVCFs (SRR7062654-A... [ 0%] 2 of 715 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d8/da3b85] process > Mpileup (SRR7062655-AADN040... [ 93%] 690 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3747) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [4e/ec35ad] process > HaplotypeCaller (SRR7062655... [ 97%] 715 of 740 [23/93e291] process > GenotypeGVCFs (SRR7062654-A... [ 2%] 15 of 715 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d8/da3b85] process > Mpileup (SRR7062655-AADN040... [ 93%] 690 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3753) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [4e/ec35ad] process > HaplotypeCaller (SRR7062655... [ 97%] 715 of 740 [22/42926c] process > GenotypeGVCFs (SRR7062654-A... [ 2%] 15 of 715 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d8/da3b85] process > Mpileup (SRR7062655-AADN040... [ 93%] 690 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3758) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [4e/ec35ad] process > HaplotypeCaller (SRR7062655... [ 97%] 715 of 740 [bb/2fa9e5] process > GenotypeGVCFs (SRR7062654-A... [ 2%] 15 of 715 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d8/da3b85] process > Mpileup (SRR7062655-AADN040... [ 93%] 690 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3760) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [4e/ec35ad] process > HaplotypeCaller (SRR7062655... [ 97%] 715 of 740 [02/7c410c] process > GenotypeGVCFs (SRR7062654-A... [ 2%] 15 of 715 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [6c/e9adc8] process > FreebayesSingle (SRR7062655... [100%] 739 of 740 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d8/da3b85] process > Mpileup (SRR7062655-AADN040... [ 93%] 690 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3762) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [4e/ec35ad] process > HaplotypeCaller (SRR7062655... [ 97%] 715 of 740 [e1/cdc049] process > GenotypeGVCFs (SRR7062654-A... [ 2%] 15 of 715 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fc/c95571] process > Mpileup (SRR7062655-AADN040... [ 93%] 691 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3762) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [4e/ec35ad] process > HaplotypeCaller (SRR7062655... [ 97%] 715 of 740 [e1/cdc049] process > GenotypeGVCFs (SRR7062654-A... [ 2%] 15 of 715 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 1 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fc/c95571] process > Mpileup (SRR7062655-AADN040... [ 93%] 691 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3762) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [4e/ec35ad] process > HaplotypeCaller (SRR7062655... [ 97%] 715 of 740 [e1/cdc049] process > GenotypeGVCFs (SRR7062654-A... [ 2%] 15 of 715 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [fc/c95571] process > Mpileup (SRR7062655-AADN040... [ 93%] 691 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3764) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [52/569d3d] process > HaplotypeCaller (SRR7062655... [ 97%] 716 of 740 [e7/0e8fc6] process > GenotypeGVCFs (SRR7062654-A... [ 2%] 15 of 716 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [e4/0881a0] process > Mpileup (SRR7062655-AADN040... [ 94%] 692 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3767) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [5c/f976db] process > HaplotypeCaller (SRR7062655... [ 97%] 717 of 740 [9b/20d6db] process > GenotypeGVCFs (SRR7062654-A... [ 2%] 15 of 717 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6d/21de32] process > Mpileup (SRR7062655-AADN040... [ 94%] 695 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3768) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [5c/f976db] process > HaplotypeCaller (SRR7062655... [ 97%] 717 of 740 [b7/926144] process > GenotypeGVCFs (SRR7062654-K... [ 2%] 15 of 717 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [6d/21de32] process > Mpileup (SRR7062655-AADN040... [ 94%] 695 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3770) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [5c/f976db] process > HaplotypeCaller (SRR7062655... [ 97%] 717 of 740 [d1/87eeb9] process > GenotypeGVCFs (SRR7062654-A... [ 2%] 15 of 717 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d0/a3fb41] process > Mpileup (SRR7062655-AADN040... [ 94%] 698 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3771) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [5c/f976db] process > HaplotypeCaller (SRR7062655... [ 97%] 717 of 740 [3b/975ca4] process > GenotypeGVCFs (SRR7062654-A... [ 2%] 15 of 717 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d0/a3fb41] process > Mpileup (SRR7062655-AADN040... [ 94%] 698 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3772) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [28/fe54f7] process > HaplotypeCaller (SRR7062655... [ 97%] 718 of 740 [f3/bd3c22] process > GenotypeGVCFs (SRR7062654-A... [ 2%] 15 of 718 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d0/a3fb41] process > Mpileup (SRR7062655-AADN040... [ 94%] 698 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3774) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [25/9ef7f8] process > HaplotypeCaller (SRR7062655... [ 97%] 719 of 740 [d5/c7f290] process > GenotypeGVCFs (SRR7062654-A... [ 3%] 25 of 719 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f2/774592] process > Mpileup (SRR7062655-AADN040... [ 95%] 701 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3779) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [25/9ef7f8] process > HaplotypeCaller (SRR7062655... [ 97%] 719 of 740 [b7/926144] process > GenotypeGVCFs (SRR7062654-K... [ 6%] 46 of 719 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f2/774592] process > Mpileup (SRR7062655-AADN040... [ 95%] 701 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3785) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [25/9ef7f8] process > HaplotypeCaller (SRR7062655... [ 97%] 719 of 740 [53/f58598] process > GenotypeGVCFs (SRR7062654-A... [ 6%] 46 of 719 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f2/774592] process > Mpileup (SRR7062655-AADN040... [ 95%] 701 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3790) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [25/9ef7f8] process > HaplotypeCaller (SRR7062655... [ 97%] 719 of 740 [36/0613cd] process > GenotypeGVCFs (SRR7062654-A... [ 6%] 46 of 719 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f2/774592] process > Mpileup (SRR7062655-AADN040... [ 95%] 701 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3796) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [25/9ef7f8] process > HaplotypeCaller (SRR7062655... [ 97%] 719 of 740 [71/0ef125] process > GenotypeGVCFs (SRR7062654-A... [ 6%] 46 of 719 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f2/774592] process > Mpileup (SRR7062655-AADN040... [ 95%] 701 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3802) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [25/9ef7f8] process > HaplotypeCaller (SRR7062655... [ 97%] 719 of 740 [a7/8f0bb8] process > GenotypeGVCFs (SRR7062654-A... [ 6%] 46 of 719 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f2/774592] process > Mpileup (SRR7062655-AADN040... [ 95%] 701 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3807) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [25/9ef7f8] process > HaplotypeCaller (SRR7062655... [ 97%] 719 of 740 [d6/f80f43] process > GenotypeGVCFs (SRR7062654-A... [ 6%] 46 of 719 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f2/774592] process > Mpileup (SRR7062655-AADN040... [ 95%] 701 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3808) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [76/f19ab2] process > HaplotypeCaller (SRR7062655... [ 97%] 720 of 740 [8c/a64b20] process > GenotypeGVCFs (SRR7062654-A... [ 6%] 46 of 720 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [f2/774592] process > Mpileup (SRR7062655-AADN040... [ 95%] 701 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3809) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [76/f19ab2] process > HaplotypeCaller (SRR7062655... [ 97%] 720 of 740 [ba/00f1b2] process > GenotypeGVCFs (SRR7062654-A... [ 6%] 46 of 720 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [27/9ec6ec] process > Mpileup (SRR7062655-AADN040... [ 95%] 702 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3810) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [76/f19ab2] process > HaplotypeCaller (SRR7062655... [ 97%] 720 of 740 [74/1f75d8] process > GenotypeGVCFs (SRR7062654-A... [ 6%] 46 of 720 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [63/8e5519] process > Mpileup (SRR7062655-AADN040... [ 95%] 703 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3810) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [76/f19ab2] process > HaplotypeCaller (SRR7062655... [ 97%] 720 of 740 [74/1f75d8] process > GenotypeGVCFs (SRR7062654-A... [ 6%] 46 of 720 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [38/4fe36c] process > Mpileup (SRR7062655-AADN040... [ 95%] 704 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3811) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [76/f19ab2] process > HaplotypeCaller (SRR7062655... [ 97%] 720 of 740 [ad/8b80cb] process > GenotypeGVCFs (SRR7062654-A... [ 6%] 46 of 720 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [38/4fe36c] process > Mpileup (SRR7062655-AADN040... [ 95%] 704 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3811) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [76/f19ab2] process > HaplotypeCaller (SRR7062655... [ 97%] 720 of 740 [ad/8b80cb] process > GenotypeGVCFs (SRR7062654-A... [ 6%] 46 of 720 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [38/4fe36c] process > Mpileup (SRR7062655-AADN040... [ 95%] 704 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3812) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [0e/8487b2] process > GenotypeGVCFs (SRR7062654-A... [ 6%] 46 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [38/4fe36c] process > Mpileup (SRR7062655-AADN040... [ 95%] 704 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3815) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [42/0304b3] process > GenotypeGVCFs (SRR7062654-A... [ 8%] 56 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [38/4fe36c] process > Mpileup (SRR7062655-AADN040... [ 95%] 704 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3820) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [6c/dca3e4] process > GenotypeGVCFs (SRR7062654-A... [ 11%] 76 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [38/4fe36c] process > Mpileup (SRR7062655-AADN040... [ 95%] 704 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3825) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [d6/145c58] process > GenotypeGVCFs (SRR7062654-A... [ 12%] 87 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [38/4fe36c] process > Mpileup (SRR7062655-AADN040... [ 95%] 704 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3830) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [12/e4edb7] process > GenotypeGVCFs (SRR7062654-A... [ 12%] 87 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [38/4fe36c] process > Mpileup (SRR7062655-AADN040... [ 95%] 704 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3836) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [0e/b068f9] process > GenotypeGVCFs (SRR7062654-A... [ 12%] 87 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [38/4fe36c] process > Mpileup (SRR7062655-AADN040... [ 95%] 704 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3841) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [dc/92f591] process > GenotypeGVCFs (SRR7062654-A... [ 12%] 87 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [38/4fe36c] process > Mpileup (SRR7062655-AADN040... [ 95%] 704 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3846) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [50/42f4cf] process > GenotypeGVCFs (SRR7062654-A... [ 12%] 87 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [38/4fe36c] process > Mpileup (SRR7062655-AADN040... [ 95%] 704 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3852) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [91/e0f275] process > GenotypeGVCFs (SRR7062654-A... [ 12%] 87 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [38/4fe36c] process > Mpileup (SRR7062655-AADN040... [ 95%] 704 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3853) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [1c/9663fa] process > GenotypeGVCFs (SRR7062654-A... [ 12%] 87 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [38/4fe36c] process > Mpileup (SRR7062655-AADN040... [ 95%] 704 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3856) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [c1/3eca45] process > GenotypeGVCFs (SRR7062654-A... [ 12%] 89 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [98/fcf45b] process > Mpileup (SRR7062655-AADN040... [ 95%] 705 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3858) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [dd/a28c9f] process > GenotypeGVCFs (SRR7062654-A... [ 12%] 89 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b2/c0b067] process > Mpileup (SRR7062655-AADN040... [ 96%] 707 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3860) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [af/e7e434] process > GenotypeGVCFs (SRR7062654-A... [ 12%] 89 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c1/76c839] process > Mpileup (SRR7062655-AADN040... [ 96%] 709 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3862) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [26/c2f6de] process > GenotypeGVCFs (SRR7062654-A... [ 12%] 89 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [09/edbaa3] process > Mpileup (SRR7062655-AADN040... [ 96%] 711 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3862) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [26/c2f6de] process > GenotypeGVCFs (SRR7062654-A... [ 12%] 89 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [09/edbaa3] process > Mpileup (SRR7062655-AADN040... [ 96%] 711 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3863) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [4b/50cccd] process > GenotypeGVCFs (SRR7062654-A... [ 12%] 89 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [bf/5afd3e] process > Mpileup (SRR7062655-AADN040... [ 96%] 712 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3863) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [0e/8487b2] process > GenotypeGVCFs (SRR7062654-A... [ 12%] 90 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [bf/5afd3e] process > Mpileup (SRR7062655-AADN040... [ 96%] 712 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3868) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [c8/0a063a] process > GenotypeGVCFs (SRR7062654-A... [ 15%] 110 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [bf/5afd3e] process > Mpileup (SRR7062655-AADN040... [ 96%] 712 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3872) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [7c/ff22b5] process > GenotypeGVCFs (SRR7062654-A... [ 18%] 127 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [bf/5afd3e] process > Mpileup (SRR7062655-AADN040... [ 96%] 712 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3876) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [ff/c93b1c] process > GenotypeGVCFs (SRR7062654-A... [ 19%] 136 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [bf/5afd3e] process > Mpileup (SRR7062655-AADN040... [ 96%] 712 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3882) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [de/26d614] process > GenotypeGVCFs (SRR7062654-K... [ 19%] 136 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [bf/5afd3e] process > Mpileup (SRR7062655-AADN040... [ 96%] 712 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3887) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [1c/a92b7f] process > GenotypeGVCFs (SRR7062654-A... [ 19%] 136 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [bf/5afd3e] process > Mpileup (SRR7062655-AADN040... [ 96%] 712 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3893) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [3c/d567c3] process > GenotypeGVCFs (SRR7062654-A... [ 19%] 136 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [bf/5afd3e] process > Mpileup (SRR7062655-AADN040... [ 96%] 712 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3899) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [11/59eef9] process > GenotypeGVCFs (SRR7062654-A... [ 19%] 136 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [bf/5afd3e] process > Mpileup (SRR7062655-AADN040... [ 96%] 712 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3905) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [4f/2f6f0e] process > GenotypeGVCFs (SRR7062654-A... [ 19%] 136 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [bf/5afd3e] process > Mpileup (SRR7062655-AADN040... [ 96%] 712 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3910) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [7e/a81a7b] process > GenotypeGVCFs (SRR7062654-K... [ 19%] 136 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [bf/5afd3e] process > Mpileup (SRR7062655-AADN040... [ 96%] 712 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3911) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [89/cb1831] process > GenotypeGVCFs (SRR7062654-A... [ 19%] 139 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8f/1adf9c] process > Mpileup (SRR7062655-AADN040... [ 96%] 713 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3914) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [29/028ee2] process > GenotypeGVCFs (SRR7062654-A... [ 19%] 139 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8f/1adf9c] process > Mpileup (SRR7062655-AADN040... [ 96%] 713 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3915) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [48/e06966] process > GenotypeGVCFs (SRR7062654-A... [ 19%] 139 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [36/a6e81e] process > Mpileup (SRR7062655-AADN040... [ 96%] 714 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3917) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [53/1b4acf] process > GenotypeGVCFs (SRR7062654-A... [ 19%] 139 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [93/d09ccd] process > Mpileup (SRR7062655-AADN040... [ 97%] 716 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3918) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [8a/95b20a] process > GenotypeGVCFs (SRR7062654-A... [ 19%] 139 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c0/62cea3] process > Mpileup (SRR7062655-AADN040... [ 97%] 717 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3918) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [8a/95b20a] process > GenotypeGVCFs (SRR7062654-A... [ 19%] 139 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c0/62cea3] process > Mpileup (SRR7062655-AADN040... [ 97%] 717 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3918) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [8a/95b20a] process > GenotypeGVCFs (SRR7062654-A... [ 19%] 139 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [c0/62cea3] process > Mpileup (SRR7062655-AADN040... [ 97%] 717 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3919) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [39/d565c2] process > GenotypeGVCFs (SRR7062654-A... [ 19%] 139 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [a7/13d733] process > Mpileup (SRR7062655-AADN040... [ 97%] 718 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3921) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [f1/e65cbd] process > GenotypeGVCFs (SRR7062654-A... [ 21%] 148 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [94/1c8edf] process > Mpileup (SRR7062655-AADN040... [ 97%] 719 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3925) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [5c/136614] process > GenotypeGVCFs (SRR7062654-A... [ 24%] 170 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [94/1c8edf] process > Mpileup (SRR7062655-AADN040... [ 97%] 719 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3929) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [29/028ee2] process > GenotypeGVCFs (SRR7062654-A... [ 26%] 189 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [94/1c8edf] process > Mpileup (SRR7062655-AADN040... [ 97%] 719 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3935) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [97/e675f9] process > GenotypeGVCFs (SRR7062654-A... [ 27%] 192 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [94/1c8edf] process > Mpileup (SRR7062655-AADN040... [ 97%] 719 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3940) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [35/5ddf5c] process > GenotypeGVCFs (SRR7062654-A... [ 27%] 192 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [94/1c8edf] process > Mpileup (SRR7062655-AADN040... [ 97%] 719 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3946) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [88/c9a139] process > GenotypeGVCFs (SRR7062654-A... [ 27%] 192 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [94/1c8edf] process > Mpileup (SRR7062655-AADN040... [ 97%] 719 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3953) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [73/76de70] process > GenotypeGVCFs (SRR7062654-A... [ 27%] 192 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [94/1c8edf] process > Mpileup (SRR7062655-AADN040... [ 97%] 719 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3960) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [5b/6acdb2] process > GenotypeGVCFs (SRR7062654-A... [ 27%] 192 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [94/1c8edf] process > Mpileup (SRR7062655-AADN040... [ 97%] 719 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3966) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [cc/c33b67] process > GenotypeGVCFs (SRR7062654-A... [ 27%] 192 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [94/1c8edf] process > Mpileup (SRR7062655-AADN040... [ 97%] 719 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3972) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [d8/3860a5] process > GenotypeGVCFs (SRR7062654-A... [ 27%] 192 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [94/1c8edf] process > Mpileup (SRR7062655-AADN040... [ 97%] 719 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3973) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [13/0edc73] process > GenotypeGVCFs (SRR7062654-A... [ 27%] 192 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [94/1c8edf] process > Mpileup (SRR7062655-AADN040... [ 97%] 719 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3976) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [32/e43c3b] process > GenotypeGVCFs (SRR7062654-A... [ 27%] 196 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [94/1c8edf] process > Mpileup (SRR7062655-AADN040... [ 97%] 719 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3977) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [c9/917979] process > GenotypeGVCFs (SRR7062654-A... [ 27%] 196 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [94/1c8edf] process > Mpileup (SRR7062655-AADN040... [ 97%] 719 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3979) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [48/155a30] process > GenotypeGVCFs (SRR7062654-A... [ 27%] 196 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [8f/be64b8] process > Mpileup (SRR7062655-AADN040... [ 97%] 721 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3981) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [ad/b6596e] process > GenotypeGVCFs (SRR7062654-A... [ 27%] 196 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b5/0a72e1] process > Mpileup (SRR7062655-AADN040... [ 98%] 723 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3981) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [ad/b6596e] process > GenotypeGVCFs (SRR7062654-A... [ 27%] 196 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b5/0a72e1] process > Mpileup (SRR7062655-AADN040... [ 98%] 723 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3981) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [ad/b6596e] process > GenotypeGVCFs (SRR7062654-A... [ 27%] 196 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [b5/0a72e1] process > Mpileup (SRR7062655-AADN040... [ 98%] 723 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3982) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [ff/1da5e6] process > GenotypeGVCFs (SRR7062654-A... [ 27%] 196 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [46/70f269] process > Mpileup (SRR7062655-AADN040... [ 98%] 724 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3983) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [94/53feb1] process > GenotypeGVCFs (SRR7062654-A... [ 29%] 211 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7d/c799c3] process > Mpileup (SRR7062655-AADN040... [ 98%] 725 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3985) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [33/6e49aa] process > GenotypeGVCFs (SRR7062654-A... [ 33%] 235 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7d/c799c3] process > Mpileup (SRR7062655-AADN040... [ 98%] 725 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3987) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [13/6bfed1] process > GenotypeGVCFs (SRR7062654-A... [ 35%] 255 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7d/c799c3] process > Mpileup (SRR7062655-AADN040... [ 98%] 725 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3990) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [f0/614228] process > GenotypeGVCFs (SRR7062654-A... [ 35%] 255 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7d/c799c3] process > Mpileup (SRR7062655-AADN040... [ 98%] 725 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (3996) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [58/5803f2] process > GenotypeGVCFs (SRR7062654-A... [ 35%] 255 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7d/c799c3] process > Mpileup (SRR7062655-AADN040... [ 98%] 725 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4001) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [24/d69e84] process > GenotypeGVCFs (SRR7062654-A... [ 35%] 255 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7d/c799c3] process > Mpileup (SRR7062655-AADN040... [ 98%] 725 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4008) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [e7/a1fb54] process > GenotypeGVCFs (SRR7062654-A... [ 35%] 255 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7d/c799c3] process > Mpileup (SRR7062655-AADN040... [ 98%] 725 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4013) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [c5/aa11ec] process > GenotypeGVCFs (SRR7062654-A... [ 35%] 255 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7d/c799c3] process > Mpileup (SRR7062655-AADN040... [ 98%] 725 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4019) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [9c/139a7d] process > GenotypeGVCFs (SRR7062654-A... [ 35%] 255 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7d/c799c3] process > Mpileup (SRR7062655-AADN040... [ 98%] 725 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4025) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [0a/16a7b2] process > GenotypeGVCFs (SRR7062654-A... [ 35%] 255 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7d/c799c3] process > Mpileup (SRR7062655-AADN040... [ 98%] 725 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4031) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [e9/54cb0c] process > GenotypeGVCFs (SRR7062654-A... [ 35%] 255 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7d/c799c3] process > Mpileup (SRR7062655-AADN040... [ 98%] 725 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4038) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [fc/0eca58] process > GenotypeGVCFs (SRR7062654-2... [ 35%] 255 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7d/c799c3] process > Mpileup (SRR7062655-AADN040... [ 98%] 725 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4042) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [c0/4d6f85] process > GenotypeGVCFs (SRR7062654-2... [ 35%] 255 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7d/c799c3] process > Mpileup (SRR7062655-AADN040... [ 98%] 725 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4043) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [48/155a30] process > GenotypeGVCFs (SRR7062654-A... [ 36%] 258 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7d/c799c3] process > Mpileup (SRR7062655-AADN040... [ 98%] 725 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4045) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [44/6e4b60] process > GenotypeGVCFs (SRR7062654-2... [ 36%] 258 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7d/c799c3] process > Mpileup (SRR7062655-AADN040... [ 98%] 725 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4046) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [8d/17a23c] process > GenotypeGVCFs (SRR7062654-2... [ 36%] 258 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [5b/065acd] process > Mpileup (SRR7062655-AADN040... [ 98%] 726 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4047) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [0d/973011] process > GenotypeGVCFs (SRR7062654-A... [ 36%] 258 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d8/288e84] process > Mpileup (SRR7062655-AADN040... [ 98%] 728 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4048) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [aa/1534ea] process > GenotypeGVCFs (SRR7062654-A... [ 36%] 258 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d8/288e84] process > Mpileup (SRR7062655-AADN040... [ 98%] 728 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4048) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [aa/1534ea] process > GenotypeGVCFs (SRR7062654-A... [ 36%] 258 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d8/288e84] process > Mpileup (SRR7062655-AADN040... [ 98%] 728 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4048) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [3c/5a4cca] process > GenotypeGVCFs (SRR7062654-A... [ 37%] 265 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [77/0638ff] process > Mpileup (SRR7062655-KQ75961... [ 99%] 729 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4049) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [e7/a1fb54] process > GenotypeGVCFs (SRR7062654-A... [ 40%] 287 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [77/0638ff] process > Mpileup (SRR7062655-KQ75961... [ 99%] 729 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4051) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [a7/d46deb] process > GenotypeGVCFs (SRR7062654-A... [ 43%] 307 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [77/0638ff] process > Mpileup (SRR7062655-KQ75961... [ 99%] 729 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4051) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [51/92d039] process > GenotypeGVCFs (SRR7062654-A... [ 44%] 317 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [77/0638ff] process > Mpileup (SRR7062655-KQ75961... [ 99%] 729 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4053) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [68/f5b949] process > GenotypeGVCFs (SRR7062654-A... [ 44%] 317 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [77/0638ff] process > Mpileup (SRR7062655-KQ75961... [ 99%] 729 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4058) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [f5/4ef31e] process > GenotypeGVCFs (SRR7062654-A... [ 44%] 317 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [77/0638ff] process > Mpileup (SRR7062655-KQ75961... [ 99%] 729 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4064) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [00/41b75c] process > GenotypeGVCFs (SRR7062654-A... [ 44%] 317 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [77/0638ff] process > Mpileup (SRR7062655-KQ75961... [ 99%] 729 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4070) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [18/e7bd01] process > GenotypeGVCFs (SRR7062654-1... [ 44%] 317 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [77/0638ff] process > Mpileup (SRR7062655-KQ75961... [ 99%] 729 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4076) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [fb/9a0456] process > GenotypeGVCFs (SRR7062654-1... [ 44%] 317 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [77/0638ff] process > Mpileup (SRR7062655-KQ75961... [ 99%] 729 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4082) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [16/3385c5] process > GenotypeGVCFs (SRR7062654-1... [ 44%] 317 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [77/0638ff] process > Mpileup (SRR7062655-KQ75961... [ 99%] 729 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4088) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [67/d2912a] process > GenotypeGVCFs (SRR7062655-K... [ 44%] 317 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [77/0638ff] process > Mpileup (SRR7062655-KQ75961... [ 99%] 729 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4094) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [6a/d4db61] process > GenotypeGVCFs (SRR7062655-A... [ 44%] 317 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [77/0638ff] process > Mpileup (SRR7062655-KQ75961... [ 99%] 729 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4100) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [a2/c6954f] process > GenotypeGVCFs (SRR7062655-3... [ 44%] 317 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [77/0638ff] process > Mpileup (SRR7062655-KQ75961... [ 99%] 729 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4106) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [43/8df07a] process > GenotypeGVCFs (SRR7062655-K... [ 44%] 317 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [77/0638ff] process > Mpileup (SRR7062655-KQ75961... [ 99%] 729 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4108) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [70/3bfd81] process > GenotypeGVCFs (SRR7062655-A... [ 44%] 317 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [77/0638ff] process > Mpileup (SRR7062655-KQ75961... [ 99%] 729 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4109) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [87/b64e1c] process > GenotypeGVCFs (SRR7062655-A... [ 44%] 318 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [18/6c8a88] process > Mpileup (SRR7062655-AADN040... [ 99%] 731 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4111) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [9d/bb36b0] process > GenotypeGVCFs (SRR7062655-A... [ 44%] 318 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [18/6c8a88] process > Mpileup (SRR7062655-AADN040... [ 99%] 731 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4114) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [77/d1433b] process > GenotypeGVCFs (SRR7062655-A... [ 44%] 320 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d2/45bfc2] process > Mpileup (SRR7062655-AADN040... [ 99%] 732 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4115) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [c4/914b0f] process > GenotypeGVCFs (SRR7062655-A... [ 45%] 321 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d2/45bfc2] process > Mpileup (SRR7062655-AADN040... [ 99%] 732 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4115) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [c4/914b0f] process > GenotypeGVCFs (SRR7062655-A... [ 45%] 321 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d2/45bfc2] process > Mpileup (SRR7062655-AADN040... [ 99%] 732 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4115) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [c4/914b0f] process > GenotypeGVCFs (SRR7062655-A... [ 45%] 321 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [d2/45bfc2] process > Mpileup (SRR7062655-AADN040... [ 99%] 732 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4115) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [c4/914b0f] process > GenotypeGVCFs (SRR7062655-A... [ 45%] 321 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [46/28f039] process > Mpileup (SRR7062655-AADN040... [ 99%] 733 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4117) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [9b/793a14] process > GenotypeGVCFs (SRR7062655-A... [ 45%] 321 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [45/2dc230] process > Mpileup (SRR7062655-AADN040... [ 99%] 734 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4117) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [8d/02d40e] process > GenotypeGVCFs (SRR7062654-2... [ 45%] 322 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [46/584e29] process > Mpileup (SRR7062655-AADN040... [ 99%] 736 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4120) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [c7/d33c38] process > GenotypeGVCFs (SRR7062655-A... [ 47%] 342 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [46/584e29] process > Mpileup (SRR7062655-AADN040... [ 99%] 736 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4121) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [70/036ab4] process > GenotypeGVCFs (SRR7062655-A... [ 50%] 358 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [46/584e29] process > Mpileup (SRR7062655-AADN040... [ 99%] 736 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4123) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [8d/18c7dc] process > GenotypeGVCFs (SRR7062655-A... [ 50%] 363 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [46/584e29] process > Mpileup (SRR7062655-AADN040... [ 99%] 736 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4125) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [00/2e46a5] process > GenotypeGVCFs (SRR7062655-A... [ 50%] 363 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [46/584e29] process > Mpileup (SRR7062655-AADN040... [ 99%] 736 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4128) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [b3/c345ee] process > GenotypeGVCFs (SRR7062655-A... [ 50%] 363 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [46/584e29] process > Mpileup (SRR7062655-AADN040... [ 99%] 736 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4134) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [36/80297f] process > GenotypeGVCFs (SRR7062655-A... [ 50%] 363 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [46/584e29] process > Mpileup (SRR7062655-AADN040... [ 99%] 736 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4138) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [fa/e7e640] process > GenotypeGVCFs (SRR7062655-K... [ 50%] 363 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [46/584e29] process > Mpileup (SRR7062655-AADN040... [ 99%] 736 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4143) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [36/232d6b] process > GenotypeGVCFs (SRR7062655-A... [ 50%] 363 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [46/584e29] process > Mpileup (SRR7062655-AADN040... [ 99%] 736 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4148) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [88/676d4f] process > GenotypeGVCFs (SRR7062655-A... [ 50%] 363 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [46/584e29] process > Mpileup (SRR7062655-AADN040... [ 99%] 736 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4153) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [2d/db18d4] process > GenotypeGVCFs (SRR7062655-A... [ 50%] 363 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [46/584e29] process > Mpileup (SRR7062655-AADN040... [ 99%] 736 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4158) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [1c/49bc9d] process > GenotypeGVCFs (SRR7062655-A... [ 50%] 363 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [46/584e29] process > Mpileup (SRR7062655-AADN040... [ 99%] 736 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4161) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [69/821348] process > GenotypeGVCFs (SRR7062655-A... [ 50%] 363 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [46/584e29] process > Mpileup (SRR7062655-AADN040... [ 99%] 736 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4163) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [6e/0bb713] process > GenotypeGVCFs (SRR7062655-K... [ 52%] 372 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [46/584e29] process > Mpileup (SRR7062655-AADN040... [ 99%] 736 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4169) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [cd/5c2ebf] process > GenotypeGVCFs (SRR7062655-A... [ 53%] 381 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [46/584e29] process > Mpileup (SRR7062655-AADN040... [ 99%] 736 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4175) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [84/0c8aaa] process > GenotypeGVCFs (SRR7062655-A... [ 53%] 381 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [46/584e29] process > Mpileup (SRR7062655-AADN040... [ 99%] 736 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4179) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [6a/7507af] process > GenotypeGVCFs (SRR7062655-A... [ 53%] 381 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [46/584e29] process > Mpileup (SRR7062655-AADN040... [ 99%] 736 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4180) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [50/1a624b] process > GenotypeGVCFs (SRR7062655-A... [ 53%] 381 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [46/584e29] process > Mpileup (SRR7062655-AADN040... [ 99%] 736 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4181) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [f3/e4a5a2] process > GenotypeGVCFs (SRR7062655-A... [ 53%] 383 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [46/584e29] process > Mpileup (SRR7062655-AADN040... [ 99%] 736 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4183) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [86/691cc6] process > GenotypeGVCFs (SRR7062655-A... [ 53%] 383 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4183) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [86/691cc6] process > GenotypeGVCFs (SRR7062655-A... [ 53%] 383 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4183) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [86/691cc6] process > GenotypeGVCFs (SRR7062655-A... [ 53%] 383 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4183) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [86/691cc6] process > GenotypeGVCFs (SRR7062655-A... [ 53%] 383 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4184) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [43/e6cc02] process > GenotypeGVCFs (SRR7062655-A... [ 53%] 384 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4185) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [60/efa405] process > GenotypeGVCFs (SRR7062655-A... [ 55%] 399 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4186) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [2d/db18d4] process > GenotypeGVCFs (SRR7062655-A... [ 58%] 417 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4187) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [d8/926267] process > GenotypeGVCFs (SRR7062655-A... [ 60%] 436 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4188) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [c7/26736c] process > GenotypeGVCFs (SRR7062655-A... [ 62%] 445 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4189) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [c4/20db3d] process > GenotypeGVCFs (SRR7062655-A... [ 62%] 445 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4190) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [f0/1bc7c7] process > GenotypeGVCFs (SRR7062655-2... [ 62%] 445 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4192) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [b0/0eb054] process > GenotypeGVCFs (SRR7062655-A... [ 62%] 445 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4194) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [ae/da78ff] process > GenotypeGVCFs (SRR7062655-A... [ 62%] 445 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4197) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [9e/497a76] process > GenotypeGVCFs (SRR7062655-A... [ 62%] 445 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4201) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [9a/9973b4] process > GenotypeGVCFs (SRR7062655-A... [ 62%] 445 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4206) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [f6/702f29] process > GenotypeGVCFs (SRR7062655-A... [ 62%] 445 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4212) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [6e/263faf] process > GenotypeGVCFs (SRR7062655-A... [ 62%] 445 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4219) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [dd/e8038e] process > GenotypeGVCFs (SRR7062655-A... [ 62%] 445 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4225) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [43/ba7cdd] process > GenotypeGVCFs (SRR7062655-A... [ 62%] 445 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4230) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [e7/6b7016] process > GenotypeGVCFs (SRR7062655-A... [ 62%] 445 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4236) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [29/df5c13] process > GenotypeGVCFs (SRR7062655-A... [ 62%] 445 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4242) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [bf/154127] process > GenotypeGVCFs (SRR7062655-A... [ 62%] 445 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4245) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [94/90a108] process > GenotypeGVCFs (SRR7062655-A... [ 62%] 445 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4249) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [b6/00063c] process > GenotypeGVCFs (SRR7062655-A... [ 63%] 453 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4253) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [84/a6658f] process > GenotypeGVCFs (SRR7062655-A... [ 63%] 453 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4253) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [18/e7bd01] process > GenotypeGVCFs (SRR7062654-1... [ 63%] 454 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4254) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [2b/9a8d4b] process > GenotypeGVCFs (SRR7062655-A... [ 63%] 454 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4254) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [da/274c93] process > GenotypeGVCFs (SRR7062654-1... [ 63%] 455 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4255) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [e2/ee519b] process > GenotypeGVCFs (SRR7062655-A... [ 63%] 455 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4256) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [1e/403d09] process > GenotypeGVCFs (SRR7062655-A... [ 63%] 456 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4256) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [1e/403d09] process > GenotypeGVCFs (SRR7062655-A... [ 63%] 456 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4256) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [1e/403d09] process > GenotypeGVCFs (SRR7062655-A... [ 63%] 456 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4256) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [24/d6be75] process > GenotypeGVCFs (SRR7062654-2... [ 64%] 458 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4258) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [c8/db6aa4] process > GenotypeGVCFs (SRR7062655-A... [ 66%] 478 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4260) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [7a/30eb98] process > GenotypeGVCFs (SRR7062655-A... [ 69%] 497 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4262) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [b6/00063c] process > GenotypeGVCFs (SRR7062655-A... [ 72%] 517 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4264) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [83/522605] process > GenotypeGVCFs (SRR7062655-A... [ 72%] 521 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4265) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [b3/1596ba] process > GenotypeGVCFs (SRR7062655-A... [ 72%] 521 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4267) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [cc/4ebcd1] process > GenotypeGVCFs (SRR7062655-A... [ 72%] 521 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4268) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [98/de1d89] process > GenotypeGVCFs (SRR7062655-A... [ 72%] 521 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4269) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [dc/c7cb0b] process > GenotypeGVCFs (SRR7062655-A... [ 72%] 521 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4273) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [a6/0341a2] process > GenotypeGVCFs (SRR7062655-A... [ 72%] 521 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4277) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [84/e28c3c] process > GenotypeGVCFs (SRR7062655-A... [ 72%] 521 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4283) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [35/d2c8cc] process > GenotypeGVCFs (SRR7062655-A... [ 72%] 521 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4289) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [f1/afa60d] process > GenotypeGVCFs (SRR7062655-A... [ 72%] 521 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4295) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [14/2c94e4] process > GenotypeGVCFs (SRR7062655-A... [ 72%] 521 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4300) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [0e/fe9797] process > GenotypeGVCFs (SRR7062655-A... [ 72%] 521 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4306) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [1e/474a16] process > GenotypeGVCFs (SRR7062655-A... [ 72%] 521 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4311) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [14/15ee72] process > GenotypeGVCFs (SRR7062655-A... [ 72%] 521 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4317) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [7f/a8a847] process > GenotypeGVCFs (SRR7062655-A... [ 72%] 521 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4321) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [1b/23ae16] process > GenotypeGVCFs (SRR7062655-A... [ 72%] 521 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4324) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [67/2afb82] process > GenotypeGVCFs (SRR7062655-A... [ 74%] 530 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4330) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [3f/621160] process > GenotypeGVCFs (SRR7062655-2... [ 74%] 530 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4334) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [5a/556f3b] process > GenotypeGVCFs (SRR7062655-A... [ 74%] 534 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4334) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [5a/556f3b] process > GenotypeGVCFs (SRR7062655-A... [ 74%] 534 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4334) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [5a/556f3b] process > GenotypeGVCFs (SRR7062655-A... [ 74%] 534 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4334) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [5a/556f3b] process > GenotypeGVCFs (SRR7062655-A... [ 74%] 534 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4334) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [5a/556f3b] process > GenotypeGVCFs (SRR7062655-A... [ 74%] 534 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4334) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [5a/556f3b] process > GenotypeGVCFs (SRR7062655-A... [ 74%] 534 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4338) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [42/3d9a1d] process > GenotypeGVCFs (SRR7062655-K... [ 76%] 550 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4342) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [00/fa736b] process > GenotypeGVCFs (SRR7062655-A... [ 79%] 570 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4343) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [fd/dd50b5] process > GenotypeGVCFs (SRR7062655-A... [ 81%] 586 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4346) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [d2/803fda] process > GenotypeGVCFs (SRR7062655-A... [ 81%] 587 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4348) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [3c/ba46b3] process > GenotypeGVCFs (SRR7062655-A... [ 81%] 587 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4350) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [fa/d02333] process > GenotypeGVCFs (SRR7062655-A... [ 81%] 587 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4351) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [ef/bd16ce] process > GenotypeGVCFs (SRR7062655-A... [ 81%] 587 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4353) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [2e/acfe18] process > GenotypeGVCFs (SRR7062655-A... [ 81%] 587 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4354) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [5b/c9c805] process > GenotypeGVCFs (SRR7062655-A... [ 81%] 587 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4356) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [ff/2f35a7] process > GenotypeGVCFs (SRR7062655-A... [ 81%] 587 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4356) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [9a/92347a] process > GenotypeGVCFs (SRR7062655-A... [ 81%] 587 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4360) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [c4/1b7747] process > GenotypeGVCFs (SRR7062655-A... [ 81%] 587 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4366) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [8c/d3f1d9] process > GenotypeGVCFs (SRR7062655-A... [ 81%] 587 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4372) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [62/39bda1] process > GenotypeGVCFs (SRR7062655-A... [ 81%] 587 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4378) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [23/043333] process > GenotypeGVCFs (SRR7062655-A... [ 81%] 587 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4384) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [38/99b77c] process > GenotypeGVCFs (SRR7062655-1... [ 81%] 587 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4387) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [a4/d094c0] process > GenotypeGVCFs (SRR7062654-7... [ 81%] 587 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4387) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [83/522605] process > GenotypeGVCFs (SRR7062655-A... [ 82%] 589 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4393) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [d9/428c5f] process > GenotypeGVCFs (SRR7062655-A... [ 84%] 608 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4399) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [14/4bdef0] process > GenotypeGVCFs (SRR7062655-A... [ 84%] 608 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4405) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [03/3fc045] process > GenotypeGVCFs (SRR7062655-A... [ 84%] 608 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4408) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [72/454e46] process > HaplotypeCaller (SRR7062655... [ 97%] 721 of 740 [81/5ea340] process > GenotypeGVCFs (SRR7062655-A... [ 84%] 608 of 721 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4409) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [29/e55508] process > HaplotypeCaller (SRR7062655... [ 98%] 722 of 740 [9d/eee27e] process > GenotypeGVCFs (SRR7062655-A... [ 84%] 608 of 722 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4410) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [29/e55508] process > HaplotypeCaller (SRR7062655... [ 98%] 722 of 740 [e9/88df5b] process > GenotypeGVCFs (SRR7062655-A... [ 84%] 609 of 722 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4410) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [29/e55508] process > HaplotypeCaller (SRR7062655... [ 98%] 722 of 740 [e9/88df5b] process > GenotypeGVCFs (SRR7062655-A... [ 84%] 609 of 722 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4410) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [29/e55508] process > HaplotypeCaller (SRR7062655... [ 98%] 722 of 740 [e9/88df5b] process > GenotypeGVCFs (SRR7062655-A... [ 84%] 609 of 722 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4410) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [29/e55508] process > HaplotypeCaller (SRR7062655... [ 98%] 722 of 740 [e9/88df5b] process > GenotypeGVCFs (SRR7062655-A... [ 84%] 609 of 722 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4412) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [29/e55508] process > HaplotypeCaller (SRR7062655... [ 98%] 722 of 740 [b1/031cc3] process > GenotypeGVCFs (SRR7062655-A... [ 86%] 619 of 722 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4417) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [29/e55508] process > HaplotypeCaller (SRR7062655... [ 98%] 722 of 740 [f4/2a37ee] process > GenotypeGVCFs (SRR7062655-A... [ 88%] 637 of 722 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4421) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [29/e55508] process > HaplotypeCaller (SRR7062655... [ 98%] 722 of 740 [41/8eb555] process > GenotypeGVCFs (SRR7062655-A... [ 88%] 638 of 722 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4427) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [29/e55508] process > HaplotypeCaller (SRR7062655... [ 98%] 722 of 740 [94/249b85] process > GenotypeGVCFs (SRR7062655-A... [ 88%] 638 of 722 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4430) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [29/e55508] process > HaplotypeCaller (SRR7062655... [ 98%] 722 of 740 [f6/0945dc] process > GenotypeGVCFs (SRR7062655-A... [ 88%] 638 of 722 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4433) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [29/e55508] process > HaplotypeCaller (SRR7062655... [ 98%] 722 of 740 [4f/d4bf84] process > GenotypeGVCFs (SRR7062655-A... [ 88%] 638 of 722 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4435) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [29/e55508] process > HaplotypeCaller (SRR7062655... [ 98%] 722 of 740 [93/5513d4] process > GenotypeGVCFs (SRR7062655-A... [ 88%] 638 of 722 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4436) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [29/e55508] process > HaplotypeCaller (SRR7062655... [ 98%] 722 of 740 [f3/05f39e] process > GenotypeGVCFs (SRR7062655-A... [ 88%] 638 of 722 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4437) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [29/e55508] process > HaplotypeCaller (SRR7062655... [ 98%] 722 of 740 [f3/05f39e] process > GenotypeGVCFs (SRR7062655-A... [ 88%] 638 of 722 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4439) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [29/e55508] process > HaplotypeCaller (SRR7062655... [ 98%] 722 of 740 [58/1d99d4] process > GenotypeGVCFs (SRR7062655-A... [ 88%] 638 of 722 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [29/9a7778] process > ConcatVCF (FreeBayes-SRR706... [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4442) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [29/e55508] process > HaplotypeCaller (SRR7062655... [ 98%] 722 of 740 [63/1eaa1c] process > GenotypeGVCFs (SRR7062655-A... [ 91%] 655 of 722 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [29/9a7778] process > ConcatVCF (FreeBayes-SRR706... [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4445) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [29/e55508] process > HaplotypeCaller (SRR7062655... [ 98%] 722 of 740 [9d/eee27e] process > GenotypeGVCFs (SRR7062655-A... [ 93%] 669 of 722 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [29/9a7778] process > ConcatVCF (FreeBayes-SRR706... [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4445) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [29/e55508] process > HaplotypeCaller (SRR7062655... [ 98%] 722 of 740 [e7/320823] process > GenotypeGVCFs (SRR7062655-A... [ 93%] 671 of 722 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [29/9a7778] process > ConcatVCF (FreeBayes-SRR706... [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4445) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [29/e55508] process > HaplotypeCaller (SRR7062655... [ 98%] 722 of 740 [e7/320823] process > GenotypeGVCFs (SRR7062655-A... [ 93%] 671 of 722 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [29/9a7778] process > ConcatVCF (FreeBayes-SRR706... [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4445) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [29/e55508] process > HaplotypeCaller (SRR7062655... [ 98%] 722 of 740 [e7/320823] process > GenotypeGVCFs (SRR7062655-A... [ 93%] 671 of 722 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [29/9a7778] process > ConcatVCF (FreeBayes-SRR706... [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4445) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [29/e55508] process > HaplotypeCaller (SRR7062655... [ 98%] 722 of 740 [26/d9153b] process > GenotypeGVCFs (SRR7062655-A... [ 94%] 678 of 722 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [29/9a7778] process > ConcatVCF (FreeBayes-SRR706... [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [9a/c30439] process > Mpileup (SRR7062655-AADN040... [100%] 738 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4445) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [29/e55508] process > HaplotypeCaller (SRR7062655... [ 98%] 722 of 740 [f6/0945dc] process > GenotypeGVCFs (SRR7062655-A... [ 97%] 697 of 722 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [29/9a7778] process > ConcatVCF (FreeBayes-SRR706... [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ba/c6b947] process > Mpileup (SRR7062655-AADN040... [100%] 739 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4445) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [29/e55508] process > HaplotypeCaller (SRR7062655... [ 98%] 722 of 740 [d7/26a8ce] process > GenotypeGVCFs (SRR7062655-A... [ 98%] 708 of 722 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [29/9a7778] process > ConcatVCF (FreeBayes-SRR706... [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ba/c6b947] process > Mpileup (SRR7062655-AADN040... [100%] 739 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4445) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [d0/de9ad9] process > HaplotypeCaller (SRR7062654... [ 98%] 723 of 740 [d7/26a8ce] process > GenotypeGVCFs (SRR7062655-A... [ 98%] 708 of 722 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [29/9a7778] process > ConcatVCF (FreeBayes-SRR706... [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ba/c6b947] process > Mpileup (SRR7062655-AADN040... [100%] 739 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4446) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [d0/de9ad9] process > HaplotypeCaller (SRR7062654... [ 98%] 723 of 740 [23/3bbcbb] process > GenotypeGVCFs (SRR7062655-1... [ 99%] 713 of 723 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [29/9a7778] process > ConcatVCF (FreeBayes-SRR706... [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ba/c6b947] process > Mpileup (SRR7062655-AADN040... [100%] 739 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4446) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [d0/de9ad9] process > HaplotypeCaller (SRR7062654... [ 98%] 723 of 740 [4e/df35b9] process > GenotypeGVCFs (SRR7062655-2... [ 99%] 714 of 723 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [29/9a7778] process > ConcatVCF (FreeBayes-SRR706... [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ba/c6b947] process > Mpileup (SRR7062655-AADN040... [100%] 739 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4448) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [d0/de9ad9] process > HaplotypeCaller (SRR7062654... [ 98%] 723 of 740 [4e/df35b9] process > GenotypeGVCFs (SRR7062655-2... [ 99%] 714 of 723 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [29/9a7778] process > ConcatVCF (FreeBayes-SRR706... [ 50%] 1 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ba/c6b947] process > Mpileup (SRR7062655-AADN040... [100%] 739 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [ 0%] 0 of 1 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [ 0%] 0 of 1 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4448) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [d0/de9ad9] process > HaplotypeCaller (SRR7062654... [ 98%] 723 of 740 [ca/32fa49] process > GenotypeGVCFs (SRR7062655-A... [ 99%] 715 of 723 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [29/9a7778] process > ConcatVCF (FreeBayes-SRR706... [ 50%] 1 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ba/c6b947] process > Mpileup (SRR7062655-AADN040... [100%] 739 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [ 0%] 0 of 1 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [ 0%] 0 of 1 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4450) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [d0/de9ad9] process > HaplotypeCaller (SRR7062654... [ 98%] 723 of 740 [ca/32fa49] process > GenotypeGVCFs (SRR7062655-A... [ 99%] 715 of 723 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ba/c6b947] process > Mpileup (SRR7062655-AADN040... [100%] 739 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [db/58c51a] process > BcftoolsStats (FreeBayes - ... [ 0%] 0 of 2 [40/27709d] process > Vcftools (FreeBayes - FreeB... [ 0%] 0 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4450) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [d0/de9ad9] process > HaplotypeCaller (SRR7062654... [ 98%] 723 of 740 [ff/1a3dde] process > GenotypeGVCFs (SRR7062655-1... [ 99%] 716 of 723 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ba/c6b947] process > Mpileup (SRR7062655-AADN040... [100%] 739 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [db/58c51a] process > BcftoolsStats (FreeBayes - ... [ 0%] 0 of 2 [40/27709d] process > Vcftools (FreeBayes - FreeB... [ 0%] 0 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4450) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [d0/de9ad9] process > HaplotypeCaller (SRR7062654... [ 98%] 723 of 740 [ff/1a3dde] process > GenotypeGVCFs (SRR7062655-1... [ 99%] 716 of 723 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ba/c6b947] process > Mpileup (SRR7062655-AADN040... [100%] 739 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [db/58c51a] process > BcftoolsStats (FreeBayes - ... [ 0%] 0 of 2 [40/27709d] process > Vcftools (FreeBayes - FreeB... [ 0%] 0 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4450) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [d0/de9ad9] process > HaplotypeCaller (SRR7062654... [ 98%] 723 of 740 [47/4ee31d] process > GenotypeGVCFs (SRR7062655-1... [ 99%] 717 of 723 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ba/c6b947] process > Mpileup (SRR7062655-AADN040... [100%] 739 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [db/58c51a] process > BcftoolsStats (FreeBayes - ... [ 0%] 0 of 2 [40/27709d] process > Vcftools (FreeBayes - FreeB... [ 0%] 0 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4450) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [d0/de9ad9] process > HaplotypeCaller (SRR7062654... [ 98%] 723 of 740 [f6/3f9469] process > GenotypeGVCFs (SRR7062655-1... [ 99%] 719 of 723 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ba/c6b947] process > Mpileup (SRR7062655-AADN040... [100%] 739 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [db/58c51a] process > BcftoolsStats (FreeBayes - ... [ 0%] 0 of 2 [40/27709d] process > Vcftools (FreeBayes - FreeB... [ 0%] 0 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4450) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [d0/de9ad9] process > HaplotypeCaller (SRR7062654... [ 98%] 723 of 740 [a3/d3eb04] process > GenotypeGVCFs (SRR7062655-1... [100%] 720 of 723 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ba/c6b947] process > Mpileup (SRR7062655-AADN040... [100%] 739 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [db/58c51a] process > BcftoolsStats (FreeBayes - ... [ 0%] 0 of 2 [40/27709d] process > Vcftools (FreeBayes - FreeB... [ 0%] 0 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4450) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [d0/de9ad9] process > HaplotypeCaller (SRR7062654... [ 98%] 723 of 740 [69/5ebef6] process > GenotypeGVCFs (SRR7062654-6... [100%] 722 of 723 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ba/c6b947] process > Mpileup (SRR7062655-AADN040... [100%] 739 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [db/58c51a] process > BcftoolsStats (FreeBayes - ... [ 0%] 0 of 2 [40/27709d] process > Vcftools (FreeBayes - FreeB... [ 0%] 0 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4450) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [d0/de9ad9] process > HaplotypeCaller (SRR7062654... [ 98%] 723 of 740 [ce/658634] process > GenotypeGVCFs (SRR7062654-9... [100%] 723 of 723 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ba/c6b947] process > Mpileup (SRR7062655-AADN040... [100%] 739 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [db/58c51a] process > BcftoolsStats (FreeBayes - ... [ 0%] 0 of 2 [40/27709d] process > Vcftools (FreeBayes - FreeB... [ 0%] 0 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4450) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [d0/de9ad9] process > HaplotypeCaller (SRR7062654... [ 98%] 723 of 740 [ce/658634] process > GenotypeGVCFs (SRR7062654-9... [100%] 723 of 723 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ba/c6b947] process > Mpileup (SRR7062655-AADN040... [100%] 739 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [db/58c51a] process > BcftoolsStats (FreeBayes - ... [ 50%] 1 of 2 [40/27709d] process > Vcftools (FreeBayes - FreeB... [ 0%] 0 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4450) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [d0/de9ad9] process > HaplotypeCaller (SRR7062654... [ 98%] 723 of 740 [ce/658634] process > GenotypeGVCFs (SRR7062654-9... [100%] 723 of 723 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ba/c6b947] process > Mpileup (SRR7062655-AADN040... [100%] 739 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [db/58c51a] process > BcftoolsStats (FreeBayes - ... [ 50%] 1 of 2 [40/27709d] process > Vcftools (FreeBayes - FreeB... [ 50%] 1 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4450) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [d0/de9ad9] process > HaplotypeCaller (SRR7062654... [ 98%] 723 of 740 [ce/658634] process > GenotypeGVCFs (SRR7062654-9... [100%] 723 of 723 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ba/c6b947] process > Mpileup (SRR7062655-AADN040... [100%] 739 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [db/58c51a] process > BcftoolsStats (FreeBayes - ... [ 50%] 1 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4450) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [d0/de9ad9] process > HaplotypeCaller (SRR7062654... [ 98%] 723 of 740 [ce/658634] process > GenotypeGVCFs (SRR7062654-9... [100%] 723 of 723 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ba/c6b947] process > Mpileup (SRR7062655-AADN040... [100%] 739 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4451) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e7/00fdb1] process > HaplotypeCaller (SRR7062655... [ 98%] 724 of 740 [06/9c49f0] process > GenotypeGVCFs (SRR7062655-1... [100%] 723 of 724 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ba/c6b947] process > Mpileup (SRR7062655-AADN040... [100%] 739 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4451) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e7/00fdb1] process > HaplotypeCaller (SRR7062655... [ 98%] 724 of 740 [06/9c49f0] process > GenotypeGVCFs (SRR7062655-1... [100%] 723 of 724 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [ba/c6b947] process > Mpileup (SRR7062655-AADN040... [100%] 739 of 740 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4451) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e7/00fdb1] process > HaplotypeCaller (SRR7062655... [ 98%] 724 of 740 [06/9c49f0] process > GenotypeGVCFs (SRR7062655-1... [100%] 723 of 724 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4452) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e7/00fdb1] process > HaplotypeCaller (SRR7062655... [ 98%] 724 of 740 [06/9c49f0] process > GenotypeGVCFs (SRR7062655-1... [100%] 723 of 724 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [0b/01bc95] process > MergeMpileup (SRR7062655) [ 0%] 0 of 2 [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4453) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e7/00fdb1] process > HaplotypeCaller (SRR7062655... [ 98%] 724 of 740 [06/9c49f0] process > GenotypeGVCFs (SRR7062655-1... [100%] 723 of 724 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [ 0%] 0 of 2 [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4453) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e7/00fdb1] process > HaplotypeCaller (SRR7062655... [ 98%] 724 of 740 [06/9c49f0] process > GenotypeGVCFs (SRR7062655-1... [100%] 723 of 724 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [ 0%] 0 of 2 [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4453) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e7/00fdb1] process > HaplotypeCaller (SRR7062655... [ 98%] 724 of 740 [06/9c49f0] process > GenotypeGVCFs (SRR7062655-1... [100%] 724 of 724 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [ 0%] 0 of 2 [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4453) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e7/00fdb1] process > HaplotypeCaller (SRR7062655... [ 98%] 724 of 740 [06/9c49f0] process > GenotypeGVCFs (SRR7062655-1... [100%] 724 of 724 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [0b/01bc95] process > MergeMpileup (SRR7062655) [ 50%] 1 of 2 [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4453) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e7/00fdb1] process > HaplotypeCaller (SRR7062655... [ 98%] 724 of 740 [06/9c49f0] process > GenotypeGVCFs (SRR7062655-1... [100%] 724 of 724 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4453) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f6/d3cd48] process > HaplotypeCaller (SRR7062655... [ 98%] 725 of 740 [06/9c49f0] process > GenotypeGVCFs (SRR7062655-1... [100%] 724 of 724 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4454) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f6/d3cd48] process > HaplotypeCaller (SRR7062655... [ 98%] 725 of 740 [df/122d73] process > GenotypeGVCFs (SRR7062655-8... [100%] 724 of 725 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4454) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f6/d3cd48] process > HaplotypeCaller (SRR7062655... [ 98%] 725 of 740 [df/122d73] process > GenotypeGVCFs (SRR7062655-8... [100%] 724 of 725 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4455) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f7/83aaf7] process > HaplotypeCaller (SRR7062655... [ 98%] 726 of 740 [cc/1e6853] process > GenotypeGVCFs (SRR7062655-9... [100%] 724 of 726 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4455) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f7/83aaf7] process > HaplotypeCaller (SRR7062655... [ 98%] 726 of 740 [cc/1e6853] process > GenotypeGVCFs (SRR7062655-9... [100%] 724 of 726 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4455) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f7/83aaf7] process > HaplotypeCaller (SRR7062655... [ 98%] 726 of 740 [df/122d73] process > GenotypeGVCFs (SRR7062655-8... [100%] 725 of 726 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4455) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [f7/83aaf7] process > HaplotypeCaller (SRR7062655... [ 98%] 726 of 740 [cc/1e6853] process > GenotypeGVCFs (SRR7062655-9... [100%] 726 of 726 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4456) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [4f/70ac3f] process > HaplotypeCaller (SRR7062655... [ 98%] 727 of 740 [5f/c9b097] process > GenotypeGVCFs (SRR7062655-7... [100%] 726 of 727 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4456) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [4f/70ac3f] process > HaplotypeCaller (SRR7062655... [ 98%] 727 of 740 [5f/c9b097] process > GenotypeGVCFs (SRR7062655-7... [100%] 726 of 727 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4456) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [4f/70ac3f] process > HaplotypeCaller (SRR7062655... [ 98%] 727 of 740 [5f/c9b097] process > GenotypeGVCFs (SRR7062655-7... [100%] 727 of 727 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4457) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [8b/5480e3] process > HaplotypeCaller (SRR7062654... [ 98%] 728 of 740 [f7/d806a3] process > GenotypeGVCFs (SRR7062654-5... [100%] 727 of 728 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4457) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [8b/5480e3] process > HaplotypeCaller (SRR7062654... [ 98%] 728 of 740 [f7/d806a3] process > GenotypeGVCFs (SRR7062654-5... [100%] 727 of 728 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4457) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [8b/5480e3] process > HaplotypeCaller (SRR7062654... [ 98%] 728 of 740 [f7/d806a3] process > GenotypeGVCFs (SRR7062654-5... [100%] 728 of 728 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4458) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [0d/5a71bd] process > HaplotypeCaller (SRR7062655... [ 99%] 729 of 740 [fc/a676f5] process > GenotypeGVCFs (SRR7062655-6... [100%] 728 of 729 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4458) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [0d/5a71bd] process > HaplotypeCaller (SRR7062655... [ 99%] 729 of 740 [fc/a676f5] process > GenotypeGVCFs (SRR7062655-6... [100%] 728 of 729 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4459) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [66/6b33b1] process > HaplotypeCaller (SRR7062654... [ 99%] 730 of 740 [92/6b8467] process > GenotypeGVCFs (SRR7062654-Z... [100%] 728 of 730 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4459) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [66/6b33b1] process > HaplotypeCaller (SRR7062654... [ 99%] 730 of 740 [92/6b8467] process > GenotypeGVCFs (SRR7062654-Z... [100%] 728 of 730 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4459) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [66/6b33b1] process > HaplotypeCaller (SRR7062654... [ 99%] 730 of 740 [fc/a676f5] process > GenotypeGVCFs (SRR7062655-6... [100%] 729 of 730 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4459) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [66/6b33b1] process > HaplotypeCaller (SRR7062654... [ 99%] 730 of 740 [92/6b8467] process > GenotypeGVCFs (SRR7062654-Z... [100%] 730 of 730 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4460) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [ae/fc8d69] process > HaplotypeCaller (SRR7062655... [ 99%] 731 of 740 [4e/2ce35e] process > GenotypeGVCFs (SRR7062655-5... [100%] 730 of 731 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4460) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [ae/fc8d69] process > HaplotypeCaller (SRR7062655... [ 99%] 731 of 740 [4e/2ce35e] process > GenotypeGVCFs (SRR7062655-5... [100%] 730 of 731 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4460) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [ae/fc8d69] process > HaplotypeCaller (SRR7062655... [ 99%] 731 of 740 [4e/2ce35e] process > GenotypeGVCFs (SRR7062655-5... [100%] 731 of 731 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4460) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [0a/bb8316] process > HaplotypeCaller (SRR7062655... [ 99%] 732 of 740 [4e/2ce35e] process > GenotypeGVCFs (SRR7062655-5... [100%] 731 of 732 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4461) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [0a/bb8316] process > HaplotypeCaller (SRR7062655... [ 99%] 732 of 740 [78/51c40c] process > GenotypeGVCFs (SRR7062655-Z... [100%] 731 of 732 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4461) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [0a/bb8316] process > HaplotypeCaller (SRR7062655... [ 99%] 732 of 740 [78/51c40c] process > GenotypeGVCFs (SRR7062655-Z... [100%] 731 of 732 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4461) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [0a/bb8316] process > HaplotypeCaller (SRR7062655... [ 99%] 732 of 740 [78/51c40c] process > GenotypeGVCFs (SRR7062655-Z... [100%] 732 of 732 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4462) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [a5/b138a2] process > HaplotypeCaller (SRR7062654... [ 99%] 733 of 740 [25/414f0e] process > GenotypeGVCFs (SRR7062654-3... [100%] 732 of 733 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4462) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [a5/b138a2] process > HaplotypeCaller (SRR7062654... [ 99%] 733 of 740 [25/414f0e] process > GenotypeGVCFs (SRR7062654-3... [100%] 732 of 733 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4462) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [a5/b138a2] process > HaplotypeCaller (SRR7062654... [ 99%] 733 of 740 [25/414f0e] process > GenotypeGVCFs (SRR7062654-3... [100%] 733 of 733 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4463) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [cd/a8fd7a] process > HaplotypeCaller (SRR7062654... [ 99%] 734 of 740 [eb/18e969] process > GenotypeGVCFs (SRR7062654-4... [100%] 733 of 734 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4463) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [cd/a8fd7a] process > HaplotypeCaller (SRR7062654... [ 99%] 734 of 740 [eb/18e969] process > GenotypeGVCFs (SRR7062654-4... [100%] 733 of 734 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4463) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [cd/a8fd7a] process > HaplotypeCaller (SRR7062654... [ 99%] 734 of 740 [eb/18e969] process > GenotypeGVCFs (SRR7062654-4... [100%] 734 of 734 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4464) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [08/b3322e] process > HaplotypeCaller (SRR7062655... [ 99%] 735 of 740 [9d/51adb4] process > GenotypeGVCFs (SRR7062655-4... [100%] 734 of 735 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4464) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [08/b3322e] process > HaplotypeCaller (SRR7062655... [ 99%] 735 of 740 [9d/51adb4] process > GenotypeGVCFs (SRR7062655-4... [100%] 734 of 735 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4464) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [08/b3322e] process > HaplotypeCaller (SRR7062655... [ 99%] 735 of 740 [9d/51adb4] process > GenotypeGVCFs (SRR7062655-4... [100%] 735 of 735 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4464) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [47/7da5c7] process > HaplotypeCaller (SRR7062655... [ 99%] 736 of 740 [9d/51adb4] process > GenotypeGVCFs (SRR7062655-4... [100%] 735 of 736 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4465) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [47/7da5c7] process > HaplotypeCaller (SRR7062655... [ 99%] 736 of 740 [54/a76c73] process > GenotypeGVCFs (SRR7062655-3... [100%] 735 of 736 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4465) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [47/7da5c7] process > HaplotypeCaller (SRR7062655... [ 99%] 736 of 740 [54/a76c73] process > GenotypeGVCFs (SRR7062655-3... [100%] 735 of 736 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4465) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [47/7da5c7] process > HaplotypeCaller (SRR7062655... [ 99%] 736 of 740 [54/a76c73] process > GenotypeGVCFs (SRR7062655-3... [100%] 736 of 736 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4465) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e7/8ec90c] process > HaplotypeCaller (SRR7062654... [100%] 737 of 740 [54/a76c73] process > GenotypeGVCFs (SRR7062655-3... [100%] 736 of 737 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4466) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e7/8ec90c] process > HaplotypeCaller (SRR7062654... [100%] 737 of 740 [c8/158a00] process > GenotypeGVCFs (SRR7062654-2... [100%] 736 of 737 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4466) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e7/8ec90c] process > HaplotypeCaller (SRR7062654... [100%] 737 of 740 [c8/158a00] process > GenotypeGVCFs (SRR7062654-2... [100%] 736 of 737 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4466) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [e7/8ec90c] process > HaplotypeCaller (SRR7062654... [100%] 737 of 740 [c8/158a00] process > GenotypeGVCFs (SRR7062654-2... [100%] 737 of 737 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4467) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [a0/bfbde3] process > HaplotypeCaller (SRR7062655... [100%] 738 of 740 [78/3fb8da] process > GenotypeGVCFs (SRR7062655-2... [100%] 737 of 738 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4467) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [a0/bfbde3] process > HaplotypeCaller (SRR7062655... [100%] 738 of 740 [78/3fb8da] process > GenotypeGVCFs (SRR7062655-2... [100%] 737 of 738 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4467) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [a0/bfbde3] process > HaplotypeCaller (SRR7062655... [100%] 738 of 740 [78/3fb8da] process > GenotypeGVCFs (SRR7062655-2... [100%] 738 of 738 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4468) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [bb/d0e11f] process > HaplotypeCaller (SRR7062654... [100%] 739 of 740 [cb/47366e] process > GenotypeGVCFs (SRR7062654-1... [100%] 738 of 739 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4468) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [bb/d0e11f] process > HaplotypeCaller (SRR7062654... [100%] 739 of 740 [cb/47366e] process > GenotypeGVCFs (SRR7062654-1... [100%] 738 of 739 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4468) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [bb/d0e11f] process > HaplotypeCaller (SRR7062654... [100%] 739 of 740 [cb/47366e] process > GenotypeGVCFs (SRR7062654-1... [100%] 739 of 739 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4468) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [cb/47366e] process > GenotypeGVCFs (SRR7062654-1... [100%] 739 of 740 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4469) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 739 of 740 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4469) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 739 of 740 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e6/f9fd98] process > ConcatVCF (FreeBayes-SRR706... [ 50%] 2 of 4 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4471) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 739 of 740 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [ed/7439fc] process > ConcatVCF (HaplotypeCallerG... [ 50%] 2 of 4 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4471) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 739 of 740 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [ed/7439fc] process > ConcatVCF (HaplotypeCallerG... [ 50%] 2 of 4 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [7f/e2816d] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4472) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 739 of 740 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [a8/e34013] process > ConcatVCF (HaplotypeCallerG... [ 75%] 3 of 4 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f5/6d32be] process > BcftoolsStats (FreeBayes - ... [ 67%] 2 of 3 [c9/ca8d32] process > Vcftools (HaplotypeCallerGV... [ 67%] 2 of 3 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4473) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 739 of 740 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [a8/e34013] process > ConcatVCF (HaplotypeCallerG... [ 75%] 3 of 4 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [a7/b6700a] process > BcftoolsStats (HaplotypeCal... [ 67%] 2 of 3 [c9/ca8d32] process > Vcftools (HaplotypeCallerGV... [ 67%] 2 of 3 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4474) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 739 of 740 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [ed/7439fc] process > ConcatVCF (HaplotypeCallerG... [100%] 4 of 4 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [a7/b6700a] process > BcftoolsStats (HaplotypeCal... [ 50%] 2 of 4 [c9/ca8d32] process > Vcftools (HaplotypeCallerGV... [ 50%] 2 of 4 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4475) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 739 of 740 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [ed/7439fc] process > ConcatVCF (HaplotypeCallerG... [100%] 4 of 4 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [52/3d374c] process > BcftoolsStats (HaplotypeCal... [ 50%] 2 of 4 [b0/cf5d42] process > Vcftools (HaplotypeCallerGV... [ 50%] 2 of 4 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4475) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 739 of 740 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [ed/7439fc] process > ConcatVCF (HaplotypeCallerG... [100%] 4 of 4 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [52/3d374c] process > BcftoolsStats (HaplotypeCal... [ 50%] 2 of 4 [b0/cf5d42] process > Vcftools (HaplotypeCallerGV... [ 50%] 2 of 4 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4475) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 740 of 740 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [ed/7439fc] process > ConcatVCF (HaplotypeCallerG... [100%] 4 of 4 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [52/3d374c] process > BcftoolsStats (HaplotypeCal... [ 50%] 2 of 4 [b0/cf5d42] process > Vcftools (HaplotypeCallerGV... [ 50%] 2 of 4 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4475) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 740 of 740 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [ed/7439fc] process > ConcatVCF (HaplotypeCallerG... [ 80%] 4 of 5 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [52/3d374c] process > BcftoolsStats (HaplotypeCal... [ 50%] 2 of 4 [b0/cf5d42] process > Vcftools (HaplotypeCallerGV... [ 50%] 2 of 4 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4476) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 740 of 740 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [5f/1b8d68] process > ConcatVCF (HaplotypeCaller-... [ 67%] 4 of 6 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [52/3d374c] process > BcftoolsStats (HaplotypeCal... [ 50%] 2 of 4 [b0/cf5d42] process > Vcftools (HaplotypeCallerGV... [ 50%] 2 of 4 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4477) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 740 of 740 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [2e/2b994b] process > ConcatVCF (HaplotypeCaller-... [ 67%] 4 of 6 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [52/3d374c] process > BcftoolsStats (HaplotypeCal... [ 50%] 2 of 4 [b0/cf5d42] process > Vcftools (HaplotypeCallerGV... [ 50%] 2 of 4 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4477) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 740 of 740 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [2e/2b994b] process > ConcatVCF (HaplotypeCaller-... [ 67%] 4 of 6 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [52/3d374c] process > BcftoolsStats (HaplotypeCal... [ 50%] 2 of 4 [b0/cf5d42] process > Vcftools (HaplotypeCallerGV... [ 50%] 2 of 4 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4478) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 740 of 740 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [2e/2b994b] process > ConcatVCF (HaplotypeCaller-... [ 83%] 5 of 6 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [52/3d374c] process > BcftoolsStats (HaplotypeCal... [ 40%] 2 of 5 [92/e6e08b] process > Vcftools (HaplotypeCaller -... [ 40%] 2 of 5 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4479) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 740 of 740 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [2e/2b994b] process > ConcatVCF (HaplotypeCaller-... [ 83%] 5 of 6 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [7e/d8199b] process > BcftoolsStats (HaplotypeCal... [ 40%] 2 of 5 [92/e6e08b] process > Vcftools (HaplotypeCaller -... [ 40%] 2 of 5 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4479) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 740 of 740 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [5f/1b8d68] process > ConcatVCF (HaplotypeCaller-... [100%] 6 of 6 ✔ [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [7e/d8199b] process > BcftoolsStats (HaplotypeCal... [ 33%] 2 of 6 [92/e6e08b] process > Vcftools (HaplotypeCaller -... [ 33%] 2 of 6 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4481) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 740 of 740 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [5f/1b8d68] process > ConcatVCF (HaplotypeCaller-... [100%] 6 of 6 ✔ [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f9/2d84ee] process > BcftoolsStats (HaplotypeCal... [ 33%] 2 of 6 [04/db9c3c] process > Vcftools (HaplotypeCaller -... [ 33%] 2 of 6 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4481) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 740 of 740 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [5f/1b8d68] process > ConcatVCF (HaplotypeCaller-... [100%] 6 of 6 ✔ [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f9/2d84ee] process > BcftoolsStats (HaplotypeCal... [ 33%] 2 of 6 [04/db9c3c] process > Vcftools (HaplotypeCaller -... [ 33%] 2 of 6 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4481) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 740 of 740 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [5f/1b8d68] process > ConcatVCF (HaplotypeCaller-... [100%] 6 of 6 ✔ [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f9/2d84ee] process > BcftoolsStats (HaplotypeCal... [ 33%] 2 of 6 [04/db9c3c] process > Vcftools (HaplotypeCaller -... [ 33%] 2 of 6 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4481) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 740 of 740 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [5f/1b8d68] process > ConcatVCF (HaplotypeCaller-... [100%] 6 of 6 ✔ [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [a7/b6700a] process > BcftoolsStats (HaplotypeCal... [ 50%] 3 of 6 [04/db9c3c] process > Vcftools (HaplotypeCaller -... [ 33%] 2 of 6 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4481) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 740 of 740 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [5f/1b8d68] process > ConcatVCF (HaplotypeCaller-... [100%] 6 of 6 ✔ [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [52/3d374c] process > BcftoolsStats (HaplotypeCal... [ 67%] 4 of 6 [04/db9c3c] process > Vcftools (HaplotypeCaller -... [ 33%] 2 of 6 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4481) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 740 of 740 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [5f/1b8d68] process > ConcatVCF (HaplotypeCaller-... [100%] 6 of 6 ✔ [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [7e/d8199b] process > BcftoolsStats (HaplotypeCal... [ 83%] 5 of 6 [04/db9c3c] process > Vcftools (HaplotypeCaller -... [ 33%] 2 of 6 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4481) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 740 of 740 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [5f/1b8d68] process > ConcatVCF (HaplotypeCaller-... [100%] 6 of 6 ✔ [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f9/2d84ee] process > BcftoolsStats (HaplotypeCal... [100%] 6 of 6 ✔ [04/db9c3c] process > Vcftools (HaplotypeCaller -... [ 33%] 2 of 6 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4481) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 740 of 740 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [5f/1b8d68] process > ConcatVCF (HaplotypeCaller-... [100%] 6 of 6 ✔ [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f9/2d84ee] process > BcftoolsStats (HaplotypeCal... [100%] 6 of 6 ✔ [92/e6e08b] process > Vcftools (HaplotypeCaller -... [ 50%] 3 of 6 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4481) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 740 of 740 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [5f/1b8d68] process > ConcatVCF (HaplotypeCaller-... [100%] 6 of 6 ✔ [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f9/2d84ee] process > BcftoolsStats (HaplotypeCal... [100%] 6 of 6 ✔ [04/db9c3c] process > Vcftools (HaplotypeCaller -... [ 67%] 4 of 6 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4481) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 740 of 740 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [5f/1b8d68] process > ConcatVCF (HaplotypeCaller-... [100%] 6 of 6 ✔ [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f9/2d84ee] process > BcftoolsStats (HaplotypeCal... [100%] 6 of 6 ✔ [c9/ca8d32] process > Vcftools (HaplotypeCallerGV... [ 83%] 5 of 6 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4481) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 740 of 740 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [5f/1b8d68] process > ConcatVCF (HaplotypeCaller-... [100%] 6 of 6 ✔ [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f9/2d84ee] process > BcftoolsStats (HaplotypeCal... [100%] 6 of 6 ✔ [b0/cf5d42] process > Vcftools (HaplotypeCallerGV... [100%] 6 of 6 ✔ [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4481) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 740 of 740 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [5f/1b8d68] process > ConcatVCF (HaplotypeCaller-... [100%] 6 of 6 ✔ [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f9/2d84ee] process > BcftoolsStats (HaplotypeCal... [100%] 6 of 6 ✔ [b0/cf5d42] process > Vcftools (HaplotypeCallerGV... [100%] 6 of 6 ✔ [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC [ 0%] 0 of 1 [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4482) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 740 of 740 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [5f/1b8d68] process > ConcatVCF (HaplotypeCaller-... [100%] 6 of 6 ✔ [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f9/2d84ee] process > BcftoolsStats (HaplotypeCal... [100%] 6 of 6 ✔ [b0/cf5d42] process > Vcftools (HaplotypeCallerGV... [100%] 6 of 6 ✔ [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [e1/1f5c95] process > MultiQC (1) [ 0%] 0 of 1 [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4482) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 740 of 740 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [5f/1b8d68] process > ConcatVCF (HaplotypeCaller-... [100%] 6 of 6 ✔ [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f9/2d84ee] process > BcftoolsStats (HaplotypeCal... [100%] 6 of 6 ✔ [b0/cf5d42] process > Vcftools (HaplotypeCallerGV... [100%] 6 of 6 ✔ [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [e1/1f5c95] process > MultiQC (1) [ 0%] 0 of 1 [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4482) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 740 of 740 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [5f/1b8d68] process > ConcatVCF (HaplotypeCaller-... [100%] 6 of 6 ✔ [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f9/2d84ee] process > BcftoolsStats (HaplotypeCal... [100%] 6 of 6 ✔ [b0/cf5d42] process > Vcftools (HaplotypeCallerGV... [100%] 6 of 6 ✔ [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [e1/1f5c95] process > MultiQC (1) [100%] 1 of 1 ✔ [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (4482) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 740 of 740 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [5f/1b8d68] process > ConcatVCF (HaplotypeCaller-... [100%] 6 of 6 ✔ [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f9/2d84ee] process > BcftoolsStats (HaplotypeCal... [100%] 6 of 6 ✔ [b0/cf5d42] process > Vcftools (HaplotypeCallerGV... [100%] 6 of 6 ✔ [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [e1/1f5c95] process > MultiQC (1) [100%] 1 of 1 ✔ [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ -[nf-core/sarek] Pipeline completed successfully- executor > slurm (4482) [bf/ce6cce] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [9f/4e1939] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [22/c13c2a] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [84/bfeadb] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [ed/2e672a] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [01/db4f1f] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [00/08a3f7] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [65/ac17f6] process > BaseRecalibrator (F_Aln-SNP... [100%] 740 of 740 ✔ [2c/01a4a7] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [a1/6b6108] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 740 of 740 ✔ [- ] process > Sentieon_BQSR - [ee/2ea18a] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [80/b53474] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [81/3820f6] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [30/94175e] process > HaplotypeCaller (SRR7062655... [100%] 740 of 740 ✔ [70/8ae5c7] process > GenotypeGVCFs (SRR7062655-1... [100%] 740 of 740 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [57/b4605a] process > FreebayesSingle (SRR7062655... [100%] 740 of 740 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [5f/1b8d68] process > ConcatVCF (HaplotypeCaller-... [100%] 6 of 6 ✔ [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [7a/07d1d2] process > Mpileup (SRR7062655-1_1-196... [100%] 740 of 740 ✔ [1c/8c90fd] process > MergeMpileup (SRR7062654) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f9/2d84ee] process > BcftoolsStats (HaplotypeCal... [100%] 6 of 6 ✔ [b0/cf5d42] process > Vcftools (HaplotypeCallerGV... [100%] 6 of 6 ✔ [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [e1/1f5c95] process > MultiQC (1) [100%] 1 of 1 ✔ [3d/4e9d92] process > Output_documentation [100%] 1 of 1 ✔ -[nf-core/sarek] Pipeline completed successfully- Completed at: 23-oct.-2021 10:10:34 Duration : 15h 28m 59s CPU hours : 462.0 Succeeded : 4'482