The workflow was completed at 2021-10-23T10:10:19.558+02:00 (duration: 15h 28m 45s)
The command used to launch the workflow was as follows:
nextflow run nf-core/sarek -c ./genotoul_1.config --input /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/input.tsv --genomes_base /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/Data/ --genome Gallus_gallus-5.0 -resume --tools HaplotypeCaller,FreeBayes,mpileup --generate_gvcf
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 |
Date Started | 2021-10-22T18:41:34.085+02:00 |
Date Completed | 2021-10-23T10:10:19.558+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