Commit 181c0f05 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Add run name param

parent 852500e6
Pipeline #3481 passed with stages
in 1 minute and 55 seconds
......@@ -4,6 +4,7 @@
// Note - $baseDir is the location of this workflow file main.nf
// Define Input variables
params.name = "small"
params.bcl = "$baseDir/../test_data/*.tar.gz"
params.designFile = "$baseDir/../test_data/design.csv"
params.outDir = "$baseDir/output"
......@@ -13,6 +14,7 @@ params.references = "$baseDir/../docs/references.md"
tarList = Channel.fromPath( params.bcl )
// Define regular variables
name = params.name
designLocation = Channel
.fromPath(params.designFile)
.ifEmpty { exit 1, "design file not found: ${params.designFile}" }
......@@ -20,8 +22,8 @@ outDir = params.outDir
references = params.references
process checkDesignFile {
tag "${bcl.baseName}"
publishDir "$outDir/misc/${task.process}/${bcl.baseName}", mode: 'copy'
tag "$name"
publishDir "$outDir/misc/${task.process}/$name", mode: 'copy'
input:
......@@ -99,9 +101,9 @@ process mkfastq {
process fastqc {
tag "${bcl.baseName}"
tag "$name"
queue 'super'
publishDir "$outDir/misc/${task.process}/${bcl.baseName}", mode: 'copy'
publishDir "$outDir/misc/${task.process}/$name", mode: 'copy'
input:
file fastqPaths
......@@ -124,8 +126,8 @@ process fastqc {
process versions {
tag "${bcl.baseName}"
publishDir "$outDir/misc/${task.process}/${bcl.baseName}", mode: 'copy'
tag "$name"
publishDir "$outDir/misc/${task.process}/$name", mode: 'copy'
input:
......@@ -149,9 +151,9 @@ process versions {
process multiqc {
tag "${bcl.baseName}"
tag "$name"
queue 'super'
publishDir "$outDir/${task.process}", mode: 'copy'
publishDir "$outDir/${task.process}/$name", mode: 'copy'
input:
......
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