From c1446208f0190ca66e73c8743334165779b6e34b Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Tue, 23 Oct 2018 15:30:06 +0200
Subject: [PATCH] BEDtools: update nf config file for PSMN
---
src/nf_modules/BEDtools/fasta_from_bed.config | 16 +++++++---------
1 file changed, 7 insertions(+), 9 deletions(-)
diff --git a/src/nf_modules/BEDtools/fasta_from_bed.config b/src/nf_modules/BEDtools/fasta_from_bed.config
index 7230def..f4b744b 100644
--- a/src/nf_modules/BEDtools/fasta_from_bed.config
+++ b/src/nf_modules/BEDtools/fasta_from_bed.config
@@ -3,23 +3,21 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $fasta_from_bed {
+ withName: fasta_from_bed {
container = "bedtools:2.25.0"
}
}
}
sge {
process{
- $fasta_from_bed {
- beforeScript = "module purge; module load BEDtools/2.25.0"
+ withName: fasta_from_bed {
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "BEDtools/2.25.0"
executor = "sge"
cpus = 1
- memory = "5GB"
- time = "6h"
- queueSize = 1000
- pollInterval = '60sec'
- queue = 'h6-E5-2667v4deb128'
- penv = 'openmp8'
+ memory = "20GB"
+ time = "12h"
+ queue = 'monointeldeb128'
}
}
}
--
GitLab