From 0d2b6e6c7a8551664e8279bb49cd801d5196e21c Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Tue, 18 Sep 2018 10:28:46 +0200
Subject: [PATCH] SNP_calling.config: create pipeline conf file
---
src/SNP_calling.config | 68 ++++++++++++++++++++++++++++++++++++++++++
1 file changed, 68 insertions(+)
create mode 100644 src/SNP_calling.config
diff --git a/src/SNP_calling.config b/src/SNP_calling.config
new file mode 100644
index 0000000..9df834d
--- /dev/null
+++ b/src/SNP_calling.config
@@ -0,0 +1,68 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $adaptor_removal {
+ container = "cutadapt:1.14"
+ }
+ $trimming {
+ container = "urqt:d62c1f8"
+ }
+ $index_fasta {
+ container = "bwa:0.7.17"
+ }
+ $mapping_fastq {
+ container = "bwa:0.7.17"
+ }
+ }
+ }
+ 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'
+ }
+ $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'
+ }
+ $index_fasta {
+ beforeScript = "module purge; module load BWA/0.7.17"
+ 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 BWA/0.7.17"
+ executor = "sge"
+ cpus = 4
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'h6-E5-2667v4deb128'
+ penv = 'openmp8'
+ }
+ }
+ }
+}
--
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