From e9012584e02292ff3b8fd649e7afc5e0d1e0edbc Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 13 Nov 2023 09:48:45 +0100
Subject: [PATCH] kmerclust.nf: remove log.txt
---
src/bin/kmerclust_clust.R | 1 +
src/bin/kmerclust_plot.R | 1 +
src/modules/kmerclust.nf | 14 ++++----------
3 files changed, 6 insertions(+), 10 deletions(-)
diff --git a/src/bin/kmerclust_clust.R b/src/bin/kmerclust_clust.R
index f13300e..5cc466e 100644
--- a/src/bin/kmerclust_clust.R
+++ b/src/bin/kmerclust_clust.R
@@ -1,3 +1,4 @@
+options(tidyverse.quiet = TRUE)
library(kmerclust)
library(tidyverse)
args <- commandArgs(trailingOnly = TRUE)
diff --git a/src/bin/kmerclust_plot.R b/src/bin/kmerclust_plot.R
index 5a62bbe..e9e9f44 100644
--- a/src/bin/kmerclust_plot.R
+++ b/src/bin/kmerclust_plot.R
@@ -1,3 +1,4 @@
+options(tidyverse.quiet = TRUE)
library(kmerclust)
library(tidyverse)
library(ggplot2)
diff --git a/src/modules/kmerclust.nf b/src/modules/kmerclust.nf
index 2811333..530c3f7 100644
--- a/src/modules/kmerclust.nf
+++ b/src/modules/kmerclust.nf
@@ -42,9 +42,7 @@ process KMERCLUST_BOOT {
script:
def args = task.ext.args ?: ''
"""
- Rscript ${projectDir}/bin/kmerclust_boot.R ${specie} ${task.cpus} ${id} \
- &> log.txt
-
+ Rscript ${projectDir}/bin/kmerclust_boot.R ${specie} ${task.cpus} ${id}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
@@ -71,8 +69,7 @@ process KMERCLUST_CLUST {
script:
def args = task.ext.args ?: ''
"""
- Rscript ${projectDir}/bin/kmerclust_clust.R ${specie} ${task.cpus} ${id} \
- &> log.txt
+ Rscript ${projectDir}/bin/kmerclust_clust.R ${specie} ${task.cpus} ${id}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
@@ -98,8 +95,7 @@ process KMERCLUST_MERGE {
script:
def args = task.ext.args ?: ''
"""
- Rscript ${projectDir}/bin/kmerclust_merge.R ${specie} \
- &> log.txt
+ Rscript ${projectDir}/bin/kmerclust_merge.R ${specie}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
@@ -125,9 +121,7 @@ process KMERCLUST_PLOT {
script:
def args = task.ext.args ?: ''
"""
- Rscript ${projectDir}/bin/kmerclust_plot.R ${specie} \
- &> log.txt
-
+ Rscript ${projectDir}/bin/kmerclust_plot.R ${specie}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
--
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