Give finishing touches after the review

This commit is contained in:
Abhinav Sharma 2020-12-08 19:08:00 +05:30
parent b56a0322ab
commit 0c9f29e0a2
4 changed files with 12 additions and 11 deletions

View file

@ -24,9 +24,8 @@ process MULTIQC {
script:
def software = getSoftwareName(task.process)
def custom_config = params.multiqc_config ? "--config $multiqc_custom_config" : ''
"""
multiqc -f $options.args $custom_config .
multiqc -f $options.args .
multiqc --version | sed -e "s/multiqc, version //g" > ${software}.version.txt
"""
}

View file

@ -33,14 +33,18 @@ input:
description: |
List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
output:
- data:
type: dir
description: MultiQC data dir
pattern: "multiqc_data"
- report:
type: file
description: MultiQC report file
pattern: "multiqc_report.html"
- data:
type: dir
description: MultiQC data dir
pattern: "multiqc_data"
- plots:
type: file
description: Plots created by MultiQC
pattern: "*_data"
- version:
type: file
description: File containing software version
@ -48,3 +52,4 @@ output:
authors:
- "@abhi18av"
- "@bunop"
- "@drpatelh"

View file

@ -5,14 +5,11 @@ nextflow.enable.dsl = 2
include { MULTIQC } from '../../../software/multiqc/main.nf' addParams(options: [publish_dir: 'test_multiqc'])
include { test_paired_end } from '../fastqc/main.nf' addParams(options: [publish_dir: 'test_paired_end'])
ch_multiqc_config = file("$launchDir/tests/software/multiqc/multiqc_config.yml", checkIfExists: true)
workflow test_multiqc {
test_paired_end()
input = [
ch_multiqc_config
.mix(test_paired_end.out.zip.collect { it[1] }.ifEmpty([]))
test_paired_end.out.zip.collect { it[1] }.ifEmpty([])
]
MULTIQC(*input)