Commit 3f1278c8 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Report fastqc's from multiple flowcells separate

parent d5ba8a06
Pipeline #3636 passed with stages
in 1 minute and 29 seconds
......@@ -4,7 +4,7 @@
// Note - $baseDir is the location of this workflow file main.nf
// Define Input variables
params.name = "small"
params.name = "run"
params.bcl = "$baseDir/../test_data/*.tar.gz"
params.designFile = "$baseDir/../test_data/design.csv"
params.outDir = "$baseDir/output"
......@@ -114,7 +114,9 @@ process fastqc {
"""
hostname
ulimit -a
find *.fastq.gz -exec mv {} $bclName.{} \\;
bash $baseDir/scripts/fastqc.sh
"""
}
......@@ -126,7 +128,6 @@ process versions {
input:
output:
file("*.yaml") into yamlPaths
......@@ -146,13 +147,13 @@ process versions {
process multiqc {
tag "$name"
queue 'super'
publishDir "$outDir/${task.process}/$name", mode: 'copy'
publishDir "$outDir/${task.process}/$name", mode: 'copy', pattern: "{multiqc*}"
module 'multiqc/1.7'
input:
file bqc name "bqc/?/*" from bqcPaths.collect()
file fqc name "fqc/?/*" from fqcPaths.collect()
file fqc name "fqc/*" from fqcPaths.collect()
file yamlPaths
output:
......
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