From 46c1f9f2f00102f117bd8615648cfafe820c698f Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Tue, 23 Oct 2018 16:44:56 +0200
Subject: [PATCH] BWA: nf update psmn config
---
src/nf_modules/BWA/indexing.config | 12 +++++-------
src/nf_modules/BWA/mapping_paired.config | 15 +++++++--------
2 files changed, 12 insertions(+), 15 deletions(-)
diff --git a/src/nf_modules/BWA/indexing.config b/src/nf_modules/BWA/indexing.config
index 7f889670..03c2f639 100644
--- a/src/nf_modules/BWA/indexing.config
+++ b/src/nf_modules/BWA/indexing.config
@@ -11,15 +11,13 @@ profiles {
psmn {
process{
withname: index_fasta {
- beforeScript = "module purge; module load BWA/0.7.17"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "BWA/0.7.17"
executor = "sge"
cpus = 1
- memory = "5GB"
- time = "6h"
- queueSize = 1000
- pollInterval = '60sec'
- queue = 'h6-E5-2667v4deb128'
- penv = 'openmp8'
+ memory = "30GB"
+ time = "12h"
+ queue = 'monointeldeb128'
}
}
}
diff --git a/src/nf_modules/BWA/mapping_paired.config b/src/nf_modules/BWA/mapping_paired.config
index d9d7a826..cbf47e27 100644
--- a/src/nf_modules/BWA/mapping_paired.config
+++ b/src/nf_modules/BWA/mapping_paired.config
@@ -11,15 +11,14 @@ profiles {
psmn {
process{
withname: mapping_fastq {
- beforeScript = "module purge; module load BWA/0.7.17"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "BWA/0.7.17"
executor = "sge"
- cpus = 4
- memory = "5GB"
- time = "6h"
- queueSize = 1000
- pollInterval = '60sec'
- queue = 'h6-E5-2667v4deb128'
- penv = 'openmp8'
+ cpus = 16
+ memory = "30GB"
+ time = "24h"
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
}
}
}
--
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