From 3d210a368b96c76d5a937230cc8b17eb14f1df02 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 10 Oct 2018 18:08:24 +0200
Subject: [PATCH] SNP_calling.nf: add SGE config
---
src/SNP_calling.config | 128 ++++++++++++++++++++++++++++++++++-------
1 file changed, 108 insertions(+), 20 deletions(-)
diff --git a/src/SNP_calling.config b/src/SNP_calling.config
index cf829ba..08d2dcd 100644
--- a/src/SNP_calling.config
+++ b/src/SNP_calling.config
@@ -53,48 +53,136 @@ profiles {
beforeScript = "module purge; module load cutadapt/1.14"
executor = "sge"
cpus = 1
- memory = "5GB"
- time = "6h"
+ memory = "20GB"
+ time = "12h"
queueSize = 1000
pollInterval = '60sec'
- queue = 'h6-E5-2667v4deb128'
- penv = 'openmp8'
+ queue = 'monointeldeb128'
}
withName: trimming {
beforeScript = "module purge; module load UrQt/d62c1f8"
executor = "sge"
- cpus = 4
+ cpus = 16
memory = "5GB"
- time = "6h"
+ time = "12h"
queueSize = 1000
pollInterval = '60sec'
- queue = 'h6-E5-2667v4deb128'
- penv = 'openmp8'
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
}
withName: index_fasta {
- beforeScript = "module purge; module load BWA/0.7.17"
+ beforeScript = "module purge; module load Bowtie2/2.3.4.1"
executor = "sge"
cpus = 1
- memory = "5GB"
+ memory = "30GB"
time = "6h"
queueSize = 1000
pollInterval = '60sec'
- queue = 'h6-E5-2667v4deb128'
- penv = 'openmp8'
+ queue = 'monointeldeb128'
}
withName: mapping_fastq {
- beforeScript = "module purge; module load BWA/0.7.17"
+ beforeScript = "module purge; module load Bowtie2/2.3.4.1"
executor = "sge"
- cpus = 4
- memory = "5GB"
- time = "6h"
+ cpus = 16
+ memory = "30GB"
+ time = "12h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
+ }
+ withName: merge_bam {
+ beforeScript = "module purge; module load sambamba/0.6.7"
+ executor = "sge"
+ cpus = 16
+ memory = "30GB"
+ time = "12h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
+ }
+ withName: sort_bam {
+ beforeScript = "module purge; module load sambamba/0.6.7"
+ executor = "sge"
+ cpus = 16
+ memory = "30GB"
+ time = "12h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
+ }
+ withName: index_bam {
+ beforeScript = "module purge; module load sambamba/0.6.7"
+ executor = "sge"
+ cpus = 16
+ memory = "30GB"
+ time = "12h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
+ }
+ withName: index2_fasta {
+ beforeScript = "module purge; module load gatk/4.0.8.1"
+ executor = "sge"
+ cpus = 1
+ memory = "20GB"
+ time = "12h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'monointeldeb128'
+ }
+ withName: index3_fasta {
+ beforeScript = "module purge; module load SAMtools/1.7"
+ executor = "sge"
+ cpus = 1
+ memory = "20GB"
+ time = "12h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'monointeldeb128'
+ }
+ withName: samtools_SNP_tumor {
+ beforeScript = "module purge; module load bcftools/1.7"
+ executor = "sge"
+ cpus = 1
+ memory = "20GB"
+ time = "12h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'monointeldeb128'
+ }
+ withName: samtools_SNP_norm {
+ beforeScript = "module purge; module load bcftools/1.7"
+ executor = "sge"
+ cpus = 1
+ memory = "20GB"
+ time = "12h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'monointeldeb128'
+ }
+ withName: vcf_to_csv_tumor {
+ beforeScript = "module purge; module load gatk/4.0.8.1"
+ executor = "sge"
+ cpus = 1
+ memory = "20GB"
+ time = "12h"
queueSize = 1000
pollInterval = '60sec'
- queue = 'h6-E5-2667v4deb128'
- penv = 'openmp8'
+ queue = 'monointeldeb128'
}
- withName: dedup_sam {
- beforeScript = "module purge; module load samblaster/0.1.24"
+ withName: vcf_to_csv_norm {
+ beforeScript = "module purge; module load gatk/4.0.8.1"
+ executor = "sge"
+ cpus = 1
+ memory = "20GB"
+ time = "12h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'monointeldeb128'
}
}
}
--
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