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