Commit ffe94839 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Remove publish dirs for intermediate processes

parent b47eead5
Pipeline #5103 failed with stages
in 5 minutes and 12 seconds
......@@ -36,7 +36,6 @@ references = params.references
process checkDesignFile {
tag "${name}"
publishDir "${outDir}/misc/${task.process}/${name}", mode: 'copy'
module 'python/3.6.1-2-anaconda'
input:
......@@ -63,7 +62,6 @@ process checkDesignFile {
process untarBCL {
tag "${tar}"
publishDir "${outDir}/${task.process}", mode: 'copy'
module 'pigz/2.4'
input:
......@@ -114,7 +112,7 @@ if (bclCount.value == 1) {
process countDesign {
tag "${name}"
publishDir "${outDir}/misc/${task.process}/${name}", mode: 'copy'
publishDir "${outDir}/${task.process}/${name}", mode: 'copy'
input:
file fastqs from cellrangerCount.collect()
......@@ -137,7 +135,6 @@ process fastqc {
tag "${bclName}"
queue 'super'
publishDir "${outDir}/misc/${task.process}/${name}/${bclName}", mode: 'copy', pattern: "{*fastqc.zip}"
module 'fastqc/0.11.5:parallel'
input:
......@@ -161,7 +158,6 @@ process fastqc {
process versions {
tag "${name}"
publishDir "${outDir}/misc/${task.process}/${name}", mode: 'copy'
module 'python/3.6.1-2-anaconda:cellranger/3.1.0:bcl2fastq/2.19.1:fastqc/0.11.5:pandoc/2.7'
input:
......
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