From cc5dda96eda826a95c043facf4f4bcd7560edc3e Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Thu, 20 Sep 2018 17:02:16 +0200
Subject: [PATCH] src/nf_modules/Hisat2/hisat2.config : nextflow configuration
file for hista2
---
src/nf_modules/Hisat2/hisat2.config | 54 +++++++++++++++++++++++++++++
1 file changed, 54 insertions(+)
create mode 100644 src/nf_modules/Hisat2/hisat2.config
diff --git a/src/nf_modules/Hisat2/hisat2.config b/src/nf_modules/Hisat2/hisat2.config
new file mode 100644
index 00000000..c2988690
--- /dev/null
+++ b/src/nf_modules/Hisat2/hisat2.config
@@ -0,0 +1,54 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $index_fasta {
+ container = "hisat2:2.0.0"
+ }
+ $mapping_fastq {
+ container = "hisat2:2.0.0"
+ }
+ $bam_converter {
+ container = "samtools:1.7"
+ }
+ }
+ }
+ sge {
+ process{
+ $index_fasta {
+ beforeScript = "module purge; module load Hisat2/2.0.0"
+ 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 Hisat2/2.0.0"
+ executor = "sge"
+ cpus = 4
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'h6-E5-2667v4deb128'
+ penv = 'openmp8'
+ }
+ $bam_converter {
+ beforeScript = "module purge; module load SAMtools/1.5"
+ executor = "sge"
+ cpus = 4
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'h6-E5-2667v4deb128'
+ penv = 'openmp8'
+ }
+ }
+ }
+}
--
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