From aee8008b7aec9480a7794c10f8b1b010e33edf4c Mon Sep 17 00:00:00 2001
From: elabaron <emmanuel.labaronne@ens-lyon.fr>
Date: Wed, 6 Jun 2018 15:01:35 +0000
Subject: [PATCH] cutadapt.config: add index and map config
---
src/cutadapt.config | 40 ++++++++++++++++++++++++++++++++++++++++
1 file changed, 40 insertions(+)
diff --git a/src/cutadapt.config b/src/cutadapt.config
index 247b34aa..7bb81606 100644
--- a/src/cutadapt.config
+++ b/src/cutadapt.config
@@ -78,3 +78,43 @@ profiles {
}
}
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $index_fasta {
+ container = "kallisto:0.43.1"
+ }
+ $mapping_fastq {
+ container = "kallisto:0.43.1"
+ }
+ }
+ }
+ sge {
+ process{
+ $index_fasta {
+ beforeScript = "module purge; module load Kallisto/0.43.1"
+ executor = "sge"
+ cpus = 1
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'h6-E5-2667v4deb128'
+ penv = 'openmp8'
+ }
+ $mapping_fastq {
+ beforeScript = "module purge; module load Kallisto/0.43.1"
+ executor = "sge"
+ cpus = 4
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'h6-E5-2667v4deb128'
+ penv = 'openmp8'
+ }
+ }
+ }
+}
--
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