From 221bd01839cb4a00c77c8e087c70f80d214a75ce Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Tue, 23 Oct 2018 16:47:07 +0200
Subject: [PATCH] Bowtie: nf update psmn config
---
src/nf_modules/Bowtie/indexing.config | 8 +++++++-
src/nf_modules/Bowtie/mapping_paired.config | 9 ++++++++-
src/nf_modules/Bowtie/mapping_single.config | 9 ++++++++-
3 files changed, 23 insertions(+), 3 deletions(-)
diff --git a/src/nf_modules/Bowtie/indexing.config b/src/nf_modules/Bowtie/indexing.config
index d97a2ad..1a0763b 100644
--- a/src/nf_modules/Bowtie/indexing.config
+++ b/src/nf_modules/Bowtie/indexing.config
@@ -11,7 +11,13 @@ profiles {
psmn {
process{
withname: index_fasta {
- beforeScript = "module purge; module load Bowtie/1.2.2"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "Bowtie/1.2.2"
+ executor = "sge"
+ cpus = 1
+ memory = "20GB"
+ time = "12h"
+ queue = 'monointeldeb128'
}
}
}
diff --git a/src/nf_modules/Bowtie/mapping_paired.config b/src/nf_modules/Bowtie/mapping_paired.config
index fbceece..a2def45 100644
--- a/src/nf_modules/Bowtie/mapping_paired.config
+++ b/src/nf_modules/Bowtie/mapping_paired.config
@@ -11,7 +11,14 @@ profiles {
psmn {
process{
withname: mapping_fastq {
- beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie/1.2.2"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "Bowtie/1.2.2:SAMtools/1.7"
+ executor = "sge"
+ cpus = 16
+ memory = "30GB"
+ time = "24h"
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
}
}
}
diff --git a/src/nf_modules/Bowtie/mapping_single.config b/src/nf_modules/Bowtie/mapping_single.config
index fbceece..a2def45 100644
--- a/src/nf_modules/Bowtie/mapping_single.config
+++ b/src/nf_modules/Bowtie/mapping_single.config
@@ -11,7 +11,14 @@ profiles {
psmn {
process{
withname: mapping_fastq {
- beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie/1.2.2"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "Bowtie/1.2.2:SAMtools/1.7"
+ executor = "sge"
+ 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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