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  |\ | |__  __ /  ` /  \ |__) |__         }  {
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  nf-core/sarek v2.7.1
----------------------------------------------------

Run Name: friendly_northcutt

## nf-core/sarek execution completed successfully! ##


The workflow was completed at 2021-10-25T14:29:20.627+02:00 (duration: 23m 24s)

The command used to launch the workflow was as follows:

  nextflow run nf-core/sarek -c ./genotoul_1.config --input /work2/project/sigenae/Formation_Aln-SNP_chr25-26/input.tsv --genomes_base /work2/project/sigenae/Formation_Aln-SNP_chr25-26/Data --genome Gallus_gallus-5.0_25-26 -resume --tools HaplotypeCaller,FreeBayes,mpileup --generate_gvcf



Pipeline Configuration:
-----------------------
 - Pipeline Release: master
 - Run Name: friendly_northcutt
 - 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/Formation_Aln-SNP_chr25-26
 - Working dir: /work2/project/sigenae/Formation_Aln-SNP_chr25-26/work
 - Script dir: /home/sigenae/.nextflow/assets/nf-core/sarek
 - User: sigenae
 - Input: /work2/project/sigenae/Formation_Aln-SNP_chr25-26/input.tsv
 - Step: mapping
 - Genome: Gallus_gallus-5.0_25-26
 - 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/Formation_Aln-SNP_chr25-26/Data
 - Save Reference: No
 - BWA indexes: /work2/project/sigenae/Formation_Aln-SNP_chr25-26/Data/Gallus_gallus.Gallus_gallus-5.0.dna.toplevel_chr25-26.fa.{amb,ann,bwt,pac,sa}
 - dict: /work2/project/sigenae/Formation_Aln-SNP_chr25-26/Data/Gallus_gallus.Gallus_gallus-5.0.dna.toplevel_chr25-26.dict
 - fasta reference: /work2/project/sigenae/Formation_Aln-SNP_chr25-26/Data/Gallus_gallus.Gallus_gallus-5.0.dna.toplevel_chr25-26.fa
 - known indels: /work2/project/sigenae/Formation_Aln-SNP_chr25-26/Data/Gallus_gallus_incl_consequences_chr25-26.vcf
 - known indels index: /work2/project/sigenae/Formation_Aln-SNP_chr25-26/Data/Gallus_gallus_incl_consequences_chr25-26.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/Formation_Aln-SNP_chr25-26/./genotoul_1.config
 - Date Started: 2021-10-25T14:05:57.107+02:00
 - Date Completed: 2021-10-25T14:29:20.627+02:00
 - Pipeline script file path: /home/sigenae/.nextflow/assets/nf-core/sarek/main.nf
 - Pipeline script hash ID: 7038b78fec38683f7c82b37e6d822ef7
 - Pipeline repository Git URL: https://github.com/nf-core/sarek
 - Pipeline repository Git Commit: 68b9930a74962f3c42eee71f51e6dd2646269199
 - Pipeline Git branch/tag: master
 - Nextflow Version: 21.04.1
 - Nextflow Build: 5556
 - Nextflow Compile Timestamp: 14-05-2021 15:20 UTC

--
nf-core/sarek
https://github.com/nf-core/sarek