From bb6bca1473d66777dbf3613d27cbb9a0df758ac8 Mon Sep 17 00:00:00 2001
From: Vincent Vanoosthuyse <vincent.vanoosthuyse@ens-lyon.fr>
Date: Mon, 23 Jul 2018 11:57:08 +0200
Subject: [PATCH] fichier de configuration cutadapt
---
src/RNAseq_sen1D.config | 67 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 67 insertions(+)
create mode 100644 src/RNAseq_sen1D.config
diff --git a/src/RNAseq_sen1D.config b/src/RNAseq_sen1D.config
new file mode 100644
index 0000000..aa27e45
--- /dev/null
+++ b/src/RNAseq_sen1D.config
@@ -0,0 +1,67 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $adaptor_removal {
+ container = "cutadapt:1.14"
+ }
+ $4_random_bases_trimming {
+ container = "cutadapt:1.14"
+ }
+ }
+ }
+ sge {
+ process{
+ $adaptor_removal {
+ beforeScript = "module purge; module load cutadapt/1.14"
+ executor = "sge"
+ cpus = 1
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'h6-E5-2667v4deb128'
+ penv = 'openmp8'
+ }
+
+ $4_random_bases_trimming {
+ beforeScript = "module purge; module load cutadapt/1.14"
+ executor = "sge"
+ cpus = 1
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'h6-E5-2667v4deb128'
+ penv = 'openmp8'
+ }
+ }
+ }
+}
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $trimming {
+ container = "urqt:d62c1f8"
+ }
+ }
+ }
+ sge {
+ process{
+ $trimming {
+ beforeScript = "module purge; module load UrQt/d62c1f8"
+ executor = "sge"
+ cpus = 4
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'h6-E5-2667v4deb128'
+ penv = 'openmp8'
+ }
+ }
+ }
+}
--
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