From e573e51f09bfd0b311eea1be9512dbe9b0840743 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 16 Apr 2019 11:26:27 +0200
Subject: [PATCH] cutadapt: add in2p3 config
---
.../cutadapt/adaptor_removal_paired.config | 15 +++++++++++++++
.../cutadapt/adaptor_removal_single.config | 15 +++++++++++++++
src/nf_modules/cutadapt/trimming_paired.config | 15 +++++++++++++++
src/nf_modules/cutadapt/trimming_single.config | 15 +++++++++++++++
4 files changed, 60 insertions(+)
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index fefbf0dd..f7d0ebbd 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -32,4 +32,19 @@ profiles {
}
}
}
+ ccin2p3 {
+ process{
+ withName: adaptor_removal {
+ beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/cutadapt/2.1/:/usr/bin:$PATH"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ memory = "10GB"
+ time = "24h"
+ }
+ }
+ }
}
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index fefbf0dd..f7d0ebbd 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -32,4 +32,19 @@ profiles {
}
}
}
+ ccin2p3 {
+ process{
+ withName: adaptor_removal {
+ beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/cutadapt/2.1/:/usr/bin:$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/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index cc3e9422..35f0963e 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -32,4 +32,19 @@ profiles {
}
}
}
+ ccin2p3 {
+ process{
+ withName: trimming {
+ beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/cutadapt/2.1/:/usr/bin:$PATH"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ memory = "10GB"
+ time = "24h"
+ }
+ }
+ }
}
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index cc3e9422..35f0963e 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -32,4 +32,19 @@ profiles {
}
}
}
+ ccin2p3 {
+ process{
+ withName: trimming {
+ beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/cutadapt/2.1/:/usr/bin:$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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