From 9ff3d2c554ef8d34edd57c0c3fc5c522fa30f242 Mon Sep 17 00:00:00 2001
From: lestrada <lilia.estrada-virrueta@ens-lyon.fr>
Date: Wed, 6 Jun 2018 14:10:38 +0000
Subject: [PATCH] RNA_Seq.config: block for cutadapt adaptor removal
---
src/RNA_Seq.config | 26 ++++++++++++++++++++++++++
1 file changed, 26 insertions(+)
create mode 100644 src/RNA_Seq.config
diff --git a/src/RNA_Seq.config b/src/RNA_Seq.config
new file mode 100644
index 0000000..aa1a372
--- /dev/null
+++ b/src/RNA_Seq.config
@@ -0,0 +1,26 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $adaptor_removal {
+ 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'
+ }
+ }
+ }
+}
--
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