From 2973fe827f0c9b224ae3b2aa65c248f82008e3fd Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Tue, 23 Oct 2018 16:31:04 +0200
Subject: [PATCH] Bowtie2: nf update config for psmn
---
src/nf_modules/Bowtie2/indexing.config | 13 ++++++++++---
src/nf_modules/Bowtie2/mapping_paired.config | 9 ++++++++-
src/nf_modules/Bowtie2/mapping_single.config | 9 ++++++++-
3 files changed, 26 insertions(+), 5 deletions(-)
diff --git a/src/nf_modules/Bowtie2/indexing.config b/src/nf_modules/Bowtie2/indexing.config
index 3b87b79e..0dc5c3a1 100644
--- a/src/nf_modules/Bowtie2/indexing.config
+++ b/src/nf_modules/Bowtie2/indexing.config
@@ -3,15 +3,22 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- withname: index_fasta {
+ withname: mapping_fastq {
container = "bowtie2:2.3.4.1"
}
}
}
psmn {
process{
- withname: index_fasta {
- beforeScript = "module purge; module load Bowtie2/2.3.4.1"
+ withname: mapping_fastq {
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "Bowtie2/2.3.4.1"
+ 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/Bowtie2/mapping_paired.config b/src/nf_modules/Bowtie2/mapping_paired.config
index 840c6d43..f97a1763 100644
--- a/src/nf_modules/Bowtie2/mapping_paired.config
+++ b/src/nf_modules/Bowtie2/mapping_paired.config
@@ -11,7 +11,14 @@ profiles {
psmn {
process{
withname: mapping_fastq {
- beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "Bowtie2/2.3.4.1: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/Bowtie2/mapping_single.config b/src/nf_modules/Bowtie2/mapping_single.config
index 840c6d43..f97a1763 100644
--- a/src/nf_modules/Bowtie2/mapping_single.config
+++ b/src/nf_modules/Bowtie2/mapping_single.config
@@ -11,7 +11,14 @@ profiles {
psmn {
process{
withname: mapping_fastq {
- beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "Bowtie2/2.3.4.1: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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