From ec7d1b21dd5ae03ae0934fdd3131c3cca0c10b07 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 10 Oct 2018 22:21:53 +0200
Subject: [PATCH] SNP_calling.config: rename some module to load
---
src/SNP_calling.config | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/src/SNP_calling.config b/src/SNP_calling.config
index 08d2dcd4..1b8640e2 100644
--- a/src/SNP_calling.config
+++ b/src/SNP_calling.config
@@ -71,7 +71,7 @@ profiles {
penv = 'openmp16'
}
withName: index_fasta {
- beforeScript = "module purge; module load Bowtie2/2.3.4.1"
+ beforeScript = "module purge; module load Bowtie2/2.3.4.1; module load sambamba/0.6.7; module load samblaster/0.6.7"
executor = "sge"
cpus = 1
memory = "30GB"
@@ -125,7 +125,7 @@ profiles {
penv = 'openmp16'
}
withName: index2_fasta {
- beforeScript = "module purge; module load gatk/4.0.8.1"
+ beforeScript = "module purge; module load GATK/4.0.8.1"
executor = "sge"
cpus = 1
memory = "20GB"
@@ -145,7 +145,7 @@ profiles {
queue = 'monointeldeb128'
}
withName: samtools_SNP_tumor {
- beforeScript = "module purge; module load bcftools/1.7"
+ beforeScript = "module purge; module load BCFtools/1.7"
executor = "sge"
cpus = 1
memory = "20GB"
@@ -155,7 +155,7 @@ profiles {
queue = 'monointeldeb128'
}
withName: samtools_SNP_norm {
- beforeScript = "module purge; module load bcftools/1.7"
+ beforeScript = "module purge; module load BCFtools/1.7"
executor = "sge"
cpus = 1
memory = "20GB"
@@ -165,7 +165,7 @@ profiles {
queue = 'monointeldeb128'
}
withName: vcf_to_csv_tumor {
- beforeScript = "module purge; module load gatk/4.0.8.1"
+ beforeScript = "module purge; module load GATK/4.0.8.1"
executor = "sge"
cpus = 1
memory = "20GB"
@@ -175,7 +175,7 @@ profiles {
queue = 'monointeldeb128'
}
withName: vcf_to_csv_norm {
- beforeScript = "module purge; module load gatk/4.0.8.1"
+ beforeScript = "module purge; module load GATK/4.0.8.1"
executor = "sge"
cpus = 1
memory = "20GB"
--
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