From 8094b470664c48f1d8b8acef82fa4c3603ffe416 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 8 Jul 2020 11:29:22 +0200
Subject: [PATCH] multiqc: fix psmn config files
---
src/nf_modules/multiqc/multiqc_paired.config | 10 ++--------
src/nf_modules/multiqc/multiqc_single.config | 17 +++++++++++------
2 files changed, 13 insertions(+), 14 deletions(-)
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index c7651b6f..2d786124 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -40,8 +40,6 @@ profiles {
cpus = 1
memory = "5GB"
time = "6h"
- queueSize = 1.70
- pollInterval = "60sec"
queue = "monointeldeb128"
}
withName: multiqc {
@@ -51,8 +49,6 @@ profiles {
cpus = 1
memory = "5GB"
time = "6h"
- queueSize = 1.70
- pollInterval = "60sec"
queue = "monointeldeb128"
}
}
@@ -68,8 +64,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r"
cpus = 1
queue = "huge"
}
@@ -79,8 +74,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r"
cpus = 1
queue = "huge"
}
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index 641a65e3..75f2f9aa 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -33,14 +33,21 @@ profiles {
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: fastqc_fastq {
+ container = "lbmc/fastqc:0.11.5"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 1
+ memory = "5GB"
+ time = "6h"
+ queue = "monointeldeb128"
+ }
+ withName: multiqc {
container = "lbmc/multiqc:1.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
memory = "5GB"
time = "6h"
- queueSize = 1.70
- pollInterval = "60sec"
queue = "monointeldeb128"
}
}
@@ -56,8 +63,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r"
cpus = 1
queue = "huge"
}
@@ -67,8 +73,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
- "
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r"
cpus = 1
queue = "huge"
}
--
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