From 0d23365b392474f90f90123e9abd4110841f6848 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Tue, 23 Oct 2018 16:56:04 +0200
Subject: [PATCH] SAMtools: nf update psmn config
---
src/nf_modules/SAMtools/filter_bams.config | 8 +++++++-
src/nf_modules/SAMtools/index_bams.config | 8 +++++++-
src/nf_modules/SAMtools/sort_bams.config | 8 +++++++-
src/nf_modules/SAMtools/split_bams.config | 8 +++++++-
4 files changed, 28 insertions(+), 4 deletions(-)
diff --git a/src/nf_modules/SAMtools/filter_bams.config b/src/nf_modules/SAMtools/filter_bams.config
index 15692631..94b96d49 100644
--- a/src/nf_modules/SAMtools/filter_bams.config
+++ b/src/nf_modules/SAMtools/filter_bams.config
@@ -11,7 +11,13 @@ profiles {
psmn {
process{
withname: filter_bam {
- beforeScript = "module purge; module load SAMtools/1.7"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "SAMtools/1.7"
+ executor = "sge"
+ cpus = 1
+ memory = "20GB"
+ time = "12h"
+ queue = 'monointeldeb128'
}
}
}
diff --git a/src/nf_modules/SAMtools/index_bams.config b/src/nf_modules/SAMtools/index_bams.config
index 277e0a36..dcc102d6 100644
--- a/src/nf_modules/SAMtools/index_bams.config
+++ b/src/nf_modules/SAMtools/index_bams.config
@@ -11,7 +11,13 @@ profiles {
psmn {
process{
withname: index_bam {
- beforeScript = "module purge; module load SAMtools/1.7"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "SAMtools/1.7"
+ executor = "sge"
+ cpus = 1
+ memory = "20GB"
+ time = "12h"
+ queue = 'monointeldeb128'
}
}
}
diff --git a/src/nf_modules/SAMtools/sort_bams.config b/src/nf_modules/SAMtools/sort_bams.config
index d961965c..14a6c7ee 100644
--- a/src/nf_modules/SAMtools/sort_bams.config
+++ b/src/nf_modules/SAMtools/sort_bams.config
@@ -11,7 +11,13 @@ profiles {
psmn {
process{
withname: sort_bam {
- beforeScript = "module purge; module load SAMtools/1.7"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "SAMtools/1.7"
+ executor = "sge"
+ cpus = 1
+ memory = "20GB"
+ time = "12h"
+ queue = 'monointeldeb128'
}
}
}
diff --git a/src/nf_modules/SAMtools/split_bams.config b/src/nf_modules/SAMtools/split_bams.config
index 43cba89e..707b20d5 100644
--- a/src/nf_modules/SAMtools/split_bams.config
+++ b/src/nf_modules/SAMtools/split_bams.config
@@ -11,7 +11,13 @@ profiles {
psmn {
process{
withname: split_bam {
- beforeScript = "module purge; module load SAMtools/1.7"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "SAMtools/1.7"
+ executor = "sge"
+ cpus = 1
+ memory = "20GB"
+ time = "12h"
+ queue = 'monointeldeb128'
}
}
}
--
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