From 82032aa929a1aba3a831f2ac34b9f7731ffeacda Mon Sep 17 00:00:00 2001
From: vvanoost <vincent.vanoosthuyse@ens-lyon.fr>
Date: Tue, 24 Jul 2018 14:28:26 +0200
Subject: [PATCH] correction SAM tools
---
src/RNAseq_sen1D.config | 20 ++++++++++++++++----
1 file changed, 16 insertions(+), 4 deletions(-)
diff --git a/src/RNAseq_sen1D.config b/src/RNAseq_sen1D.config
index 6f99548..d02f959 100644
--- a/src/RNAseq_sen1D.config
+++ b/src/RNAseq_sen1D.config
@@ -94,10 +94,16 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $sort_bam {
+ $sort_bam_forward {
container = "samtools:1.7"
}
- $index_bam {
+ $index_bam_forward {
+ container = "samtools:1.7"
+ }
+ $sort_bam_reverse {
+ container = "samtools:1.7"
+ }
+ $index_bam_reverse {
container = "samtools:1.7"
}
$split_bam {
@@ -107,10 +113,16 @@ profiles {
}
sge {
process{
- $trimming {
+ $sort_bam_forward {
+ beforeScript = "module purge; module load SAMtools/1.7"
+ }
+ $index_bam_forward {
+ beforeScript = "module purge; module load SAMtools/1.7"
+ }
+ $sort_bam_reverse {
beforeScript = "module purge; module load SAMtools/1.7"
}
- $index_bam {
+ $index_bam_reverse {
beforeScript = "module purge; module load SAMtools/1.7"
}
$split_bam {
--
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