From a0f7c6dc2a74fa48998232f7d773378ece3a7ae8 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 16 Apr 2019 13:31:36 +0200
Subject: [PATCH] sambamba: add in2p3 config
---
src/nf_modules/sambamba/index_bams.config | 15 +++++++++++++++
src/nf_modules/sambamba/sort_bams.config | 15 +++++++++++++++
src/nf_modules/sambamba/split_bams.config | 15 +++++++++++++++
3 files changed, 45 insertions(+)
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index 06c3fcc5..dd88348a 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -33,4 +33,19 @@ profiles {
}
}
}
+ ccin2p3 {
+ process{
+ withName: index_bam {
+ beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/sambamba/0.6.7/:/usr/bin:$PATH"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ memory = "10GB"
+ time = "24h"
+ }
+ }
+ }
}
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index 73f2bcd1..fe605cf4 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -33,4 +33,19 @@ profiles {
}
}
}
+ ccin2p3 {
+ process{
+ withName: sort_bam {
+ beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/sambamba/0.6.7/:/usr/bin:$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"
+ }
+ }
+ }
}
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index 95173ec2..087a0dd5 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -33,4 +33,19 @@ profiles {
}
}
}
+ ccin2p3 {
+ process{
+ withName: split_bam {
+ beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/sambamba/0.6.7/:/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"
+ }
+ }
+ }
}
--
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