From 7ff1d2c3c3310c23e1600ab2cf519882dacf3346 Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Sat, 7 May 2022 21:56:52 +0200
Subject: [PATCH] [LINT] move to 4 spaces
---
bin/src/cutsite_trimming.cpp | 2 +-
conf/igenomes.config | 4 ++--
conf/modules.config | 12 ++++++------
lib/WorkflowHic.groovy | 2 +-
modules/local/hicexplorer/hicFindTADs.nf | 4 ++--
modules/local/hicpro/combine_mates.nf | 2 +-
6 files changed, 13 insertions(+), 13 deletions(-)
diff --git a/bin/src/cutsite_trimming.cpp b/bin/src/cutsite_trimming.cpp
index 5cccebf..c7b6608 100644
--- a/bin/src/cutsite_trimming.cpp
+++ b/bin/src/cutsite_trimming.cpp
@@ -138,6 +138,6 @@ int main(int argc, char* argv[])
int trim_count=trim_fastq(fastqFile, cutSites, outFile, rmuntrim);
printf("\n##Trimmed reads: %d\n", trim_count);
return(0);
- }
+}
diff --git a/conf/igenomes.config b/conf/igenomes.config
index 3b50325..8b49d08 100644
--- a/conf/igenomes.config
+++ b/conf/igenomes.config
@@ -124,8 +124,8 @@ params {
bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/"
}
'canFam3' {
- fasta = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa"
- bowtie2 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/"
+ fasta = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa"
+ bowtie2 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/"
}
'danRer10' {
fasta = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa"
diff --git a/conf/modules.config b/conf/modules.config
index 13eb114..06aaba2 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -239,12 +239,12 @@ process {
}
withName: 'COOLER_ZOOMIFY' {
- publishDir = [
- path: { "${params.outdir}/contact_maps/cool/" },
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
- mode: 'copy'
- ]
- ext.args = "--balance"
+ publishDir = [
+ path: { "${params.outdir}/contact_maps/cool/" },
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+ mode: 'copy'
+ ]
+ ext.args = "--balance"
}
//********************************
diff --git a/lib/WorkflowHic.groovy b/lib/WorkflowHic.groovy
index d2fae92..b4755f4 100755
--- a/lib/WorkflowHic.groovy
+++ b/lib/WorkflowHic.groovy
@@ -13,7 +13,7 @@ class WorkflowHic {
// digestion parameters
if (params.digest && params.digestion && !params.digest.containsKey(params.digestion)) {
log.error "Unknown digestion protocol. Currently, the available digestion options are ${params.digest.keySet().join(", ")}. Please set manually the '--restriction_site' and '--ligation_site' parameters."
- System.exit(1)
+ System.exit(1)
}
// Check Digestion or DNase Hi-C mode
diff --git a/modules/local/hicexplorer/hicFindTADs.nf b/modules/local/hicexplorer/hicFindTADs.nf
index a6705e2..6946e63 100644
--- a/modules/local/hicexplorer/hicFindTADs.nf
+++ b/modules/local/hicexplorer/hicFindTADs.nf
@@ -23,8 +23,8 @@ process HIC_FIND_TADS {
"""
hicFindTADs --matrix ${cool} \
--outPrefix ${prefix}_hicfindtads \
- ${args} \
- --numberOfProcessors ${task.cpus}
+ ${args} \
+ --numberOfProcessors ${task.cpus}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
diff --git a/modules/local/hicpro/combine_mates.nf b/modules/local/hicpro/combine_mates.nf
index 5d92f4b..83b18dc 100644
--- a/modules/local/hicpro/combine_mates.nf
+++ b/modules/local/hicpro/combine_mates.nf
@@ -4,7 +4,7 @@ process COMBINE_MATES {
conda (params.enable_conda ? "conda-forge::python=3.9 bioconda::pysam=0.19.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
+ 'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"
input:
--
GitLab