From dbfba055dff98c21275353ae9bf6ee202b04edd0 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 10 Nov 2023 09:31:23 +0100
Subject: [PATCH] kmerclust.nf: redirect warning to log.txt
---
src/modules/kmerclust.nf | 14 ++++++++++----
1 file changed, 10 insertions(+), 4 deletions(-)
diff --git a/src/modules/kmerclust.nf b/src/modules/kmerclust.nf
index 6cc0a7e..518c730 100644
--- a/src/modules/kmerclust.nf
+++ b/src/modules/kmerclust.nf
@@ -42,7 +42,9 @@ process KMERCLUST_BOOT {
script:
def args = task.ext.args ?: ''
"""
- Rscript ${projectDir}/bin/kmerclust_boot.R ${specie} ${task.cpus} ${id}
+ Rscript ${projectDir}/bin/kmerclust_boot.R ${specie} ${task.cpus} ${id} \
+ &> log.txt
+
cat <<-END_VERSIONS > versions.yml
"${task.process}":
@@ -68,7 +70,8 @@ process KMERCLUST_CLUST {
script:
def args = task.ext.args ?: ''
"""
- Rscript ${projectDir}/bin/kmerclust_clust.R ${specie} ${task.cpus} ${id}
+ Rscript ${projectDir}/bin/kmerclust_clust.R ${specie} ${task.cpus} ${id} \
+ &> log.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
@@ -94,7 +97,8 @@ process KMERCLUST_MERGE {
script:
def args = task.ext.args ?: ''
"""
- Rscript ${projectDir}/bin/kmerclust_merge.R ${specie}
+ Rscript ${projectDir}/bin/kmerclust_merge.R ${specie} \
+ &> log.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
@@ -120,7 +124,9 @@ process KMERCLUST_PLOT {
script:
def args = task.ext.args ?: ''
"""
- Rscript ${projectDir}/bin/kmerclust_plot.R ${specie}
+ Rscript ${projectDir}/bin/kmerclust_plot.R ${specie} \
+ &> log.txt
+
cat <<-END_VERSIONS > versions.yml
"${task.process}":
--
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