From 5b50ecea03f85f45584869e8c31d910dc0659e50 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 16 Apr 2019 11:22:59 +0200
Subject: [PATCH] bowtie2: add in2p3 config
---
src/nf_modules/bowtie2/indexing.config | 15 +++++++++++++++
src/nf_modules/bowtie2/mapping_paired.config | 15 +++++++++++++++
src/nf_modules/bowtie2/mapping_single.config | 15 +++++++++++++++
3 files changed, 45 insertions(+)
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 6a9d6071..80de2148 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -33,4 +33,19 @@ profiles {
}
}
}
+ ccin2p3 {
+ process{
+ withName: index_fasta {
+ beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bowtie2/2.3.4.1/:/usr/bin:$PATH"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ memory = "10GB"
+ time = "24h"
+ }
+ }
+ }
}
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index 63ba18af..44adb9a5 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -33,4 +33,19 @@ profiles {
}
}
}
+ ccin2p3 {
+ process{
+ withName: mapping_fastq {
+ beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bowtie2/2.3.4.1/:/usr/bin:$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/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index 63ba18af..44adb9a5 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -33,4 +33,19 @@ profiles {
}
}
}
+ ccin2p3 {
+ process{
+ withName: mapping_fastq {
+ beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bowtie2/2.3.4.1/:/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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