From 7e5b25f3dc6923d1758122cb544f40a7c0a2e59a Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 16 Apr 2019 11:42:36 +0200
Subject: [PATCH] htseq: add in2p3 config
---
src/nf_modules/htseq/htseq.config | 26 ++++++++++++++++++++++++++
1 file changed, 26 insertions(+)
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index bd55d6a6..f3667f4f 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -46,4 +46,30 @@ profiles {
}
}
}
+ ccin2p3 {
+ process{
+ withName: sort_bam {
+ beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/samtools/1.7/:/usr/bin:$PATH"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ memory = "10GB"
+ time = "24h"
+ }
+ withName: trimming {
+ beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/htseq/0.11.2/:/usr/bin:$PATH"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ memory = "10GB"
+ time = "24h"
+ }
+ }
+ }
}
--
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