From dcde66592de40e31e102cb12dfcad113040b3882 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Mon, 24 Sep 2018 16:34:37 +0200
Subject: [PATCH] SNP_calling.config: add docker configs
---
src/SNP_calling.config | 37 +++++++++++++++++++++++++++++--------
1 file changed, 29 insertions(+), 8 deletions(-)
diff --git a/src/SNP_calling.config b/src/SNP_calling.config
index 9df834d..fab3005 100644
--- a/src/SNP_calling.config
+++ b/src/SNP_calling.config
@@ -3,23 +3,41 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $adaptor_removal {
+ withName: adaptor_removal {
container = "cutadapt:1.14"
}
- $trimming {
+ withName: trimming {
container = "urqt:d62c1f8"
}
- $index_fasta {
+ withName: index_fasta {
container = "bwa:0.7.17"
}
- $mapping_fastq {
+ withName: mapping_fastq {
container = "bwa:0.7.17"
}
+ withName: dedup_sam {
+ container = "samblaster:0.1.24"
+ }
+ withName: sort_bam {
+ container = "sambamba:0.6.7"
+ }
+ withName: index_bam {
+ container = "sambamba:0.6.7"
+ }
+ withName: index2_fasta {
+ container = "gatk:4.0.8.1"
+ }
+ withName: index3_fasta {
+ container = "samtools:1.7"
+ }
+ withName: HaplotypeCaller {
+ container = "gatk:4.0.8.1"
+ }
}
}
sge {
process{
- $adaptor_removal {
+ withName: adaptor_removal {
beforeScript = "module purge; module load cutadapt/1.14"
executor = "sge"
cpus = 1
@@ -30,7 +48,7 @@ profiles {
queue = 'h6-E5-2667v4deb128'
penv = 'openmp8'
}
- $trimming {
+ withName: trimming {
beforeScript = "module purge; module load UrQt/d62c1f8"
executor = "sge"
cpus = 4
@@ -41,7 +59,7 @@ profiles {
queue = 'h6-E5-2667v4deb128'
penv = 'openmp8'
}
- $index_fasta {
+ withName: index_fasta {
beforeScript = "module purge; module load BWA/0.7.17"
executor = "sge"
cpus = 1
@@ -52,7 +70,7 @@ profiles {
queue = 'h6-E5-2667v4deb128'
penv = 'openmp8'
}
- $mapping_fastq {
+ withName: mapping_fastq {
beforeScript = "module purge; module load BWA/0.7.17"
executor = "sge"
cpus = 4
@@ -63,6 +81,9 @@ profiles {
queue = 'h6-E5-2667v4deb128'
penv = 'openmp8'
}
+ withName: dedup_sam {
+ beforeScript = "module purge; module load samblaster/0.1.24"
+ }
}
}
}
--
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