From edaf1c18faacc3bedb2c5891516cbaff5032ee58 Mon Sep 17 00:00:00 2001
From: vvanoost <vincent.vanoosthuyse@ens-lyon.fr>
Date: Tue, 24 Jul 2018 13:26:31 +0200
Subject: [PATCH] add SAM tools
---
src/RNAseq_sen1D.config | 30 ++++++++++++++++++++++++++++++
1 file changed, 30 insertions(+)
diff --git a/src/RNAseq_sen1D.config b/src/RNAseq_sen1D.config
index 04de4a7..6f99548 100644
--- a/src/RNAseq_sen1D.config
+++ b/src/RNAseq_sen1D.config
@@ -89,3 +89,33 @@ profiles {
}
}
}
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $sort_bam {
+ container = "samtools:1.7"
+ }
+ $index_bam {
+ container = "samtools:1.7"
+ }
+ $split_bam {
+ container = "samtools:1.7"
+ }
+ }
+ }
+ sge {
+ process{
+ $trimming {
+ beforeScript = "module purge; module load SAMtools/1.7"
+ }
+ $index_bam {
+ beforeScript = "module purge; module load SAMtools/1.7"
+ }
+ $split_bam {
+ beforeScript = "module purge; module load SAMtools/1.7"
+ }
+ }
+ }
+}
--
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