Commit 42ddd6e9 authored by Gervaise Henry's avatar Gervaise Henry 🤠

Minor formatting

parent 36f91741
Pipeline #4267 passed with stages
in 2 minutes and 19 seconds
......@@ -12,10 +12,11 @@ params.multiqcConf = "$baseDir/conf/multiqc_config.yaml"
params.references = "$baseDir/../docs/references.md"
// Define List of Files
tarList = Channel.fromPath( params.bcl )
tarList = Channel
.fromPath( params.bcl )
bclCount = Channel
.fromPath( params.bcl )
.count()
.fromPath( params.bcl )
.count()
// Define regular variables
name = params.name
......@@ -26,6 +27,7 @@ outDir = params.outDir
multiqcConf = params.multiqcConf
references = params.references
process checkDesignFile {
tag "$name"
publishDir "$outDir/misc/${task.process}/$name", mode: 'copy'
......@@ -66,6 +68,7 @@ process untarBCL {
"""
}
process mkfastq {
tag "${bcl.baseName}"
queue '128GB,256GB,256GBv1,384GB'
......@@ -90,6 +93,7 @@ process mkfastq {
"""
}
if (bclCount.value == 1) {
process countDesign {
tag "$name"
......@@ -109,6 +113,7 @@ if (bclCount.value == 1) {
}
}
process fastqc {
tag "$bclName"
queue 'super'
......@@ -128,7 +133,6 @@ process fastqc {
ulimit -a
find *.fastq.gz -exec mv {} $bclName.{} \\;
bash "$baseDir/scripts/fastqc.sh"
"""
}
......@@ -155,6 +159,7 @@ process versions {
"""
}
process multiqc {
tag "$name"
queue 'super'
......
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