From 9d8b2010764af8e2c98e9afa8aa031b6f9b30e0d Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 16 Apr 2019 13:34:17 +0200
Subject: [PATCH] samtools: add in2p3 config
---
src/nf_modules/samtools/filter_bams.config | 15 +++++++++++++++
src/nf_modules/samtools/index_bams.config | 15 +++++++++++++++
src/nf_modules/samtools/sort_bams.config | 15 +++++++++++++++
src/nf_modules/samtools/split_bams.config | 15 +++++++++++++++
4 files changed, 60 insertions(+)
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index 2b3a814a..c8bab8db 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -33,4 +33,19 @@ profiles {
}
}
}
+ ccin2p3 {
+ process{
+ withName: filter_bam {
+ beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/samtools/1.7/:/usr/bin:$PATH"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ memory = "10GB"
+ time = "24h"
+ }
+ }
+ }
}
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index 5cec951b..89c223b4 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/src/nf_modules/samtools/index_bams.config
@@ -32,4 +32,19 @@ profiles {
}
}
}
+ ccin2p3 {
+ process{
+ withName: index_bam {
+ beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/samtools/1.7/:/usr/bin:$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"
+ }
+ }
+ }
}
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index 9f420077..6d30cc5b 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -33,4 +33,19 @@ profiles {
}
}
}
+ ccin2p3 {
+ process{
+ withName: sort_bam {
+ beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/samtools/1.7/:/usr/bin:$PATH"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ memory = "10GB"
+ time = "24h"
+ }
+ }
+ }
}
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index 91b2f1ac..9cd8b166 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -32,4 +32,19 @@ profiles {
}
}
}
+ ccin2p3 {
+ process{
+ withName: split_bam {
+ beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/samtools/1.7/:/usr/bin:$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"
+ }
+ }
+ }
}
--
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