From 14164fee7ead9fe753ff27789593f92b26f65bc8 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Tue, 23 Oct 2018 16:42:33 +0200
Subject: [PATCH] sambamba: nf update psmn config
---
src/nf_modules/sambamba/index_bams.config | 9 ++++++++-
src/nf_modules/sambamba/sort_bams.config | 9 ++++++++-
src/nf_modules/sambamba/split_bams.config | 9 ++++++++-
3 files changed, 24 insertions(+), 3 deletions(-)
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index 2e41921..e4eeaa0 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -11,7 +11,14 @@ profiles {
psmn {
process{
withname: index_bam {
- beforeScript = "module purge; module load sambamba/0.6.7"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "sambamba/0.6.7"
+ 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/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index 041a7c7..5c03e74 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -11,7 +11,14 @@ profiles {
psmn {
process{
withname: sort_bam {
- beforeScript = "module purge; module load sambamba/0.6.7"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "sambamba/0.6.7"
+ 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/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index 1f10cb4..dc0b2d3 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -11,7 +11,14 @@ profiles {
psmn {
process{
withname: split_bam {
- beforeScript = "module purge; module load sambamba/0.6.7"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "sambamba/0.6.7"
+ 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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