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Iterate again on MultiQC

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This commit is contained in:
Abhinav Sharma 2020-12-04 12:11:17 +05:30
parent 84c0bda00e
commit a30df8a59b
2 changed files with 15 additions and 9 deletions
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16
software/multiqc/main.nf
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@ -9,22 +9,24 @@ process MULTIQC {
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
saveAs: { filename -> saveFiles(filename: filename, options: params.options, publish_dir: getSoftwareName(task.process), publish_id: '') }
conda (params.enable_conda ? "bioconda::multiqc=1.9" : null)
conda(params.enable_conda ? "bioconda::multiqc=1.9" : null)
container "quay.io/biocontainers/multiqc:1.9--pyh9f0ad1d_0"
input:
tuple val(meta), path(reads)
// path multiqc_config
// path multiqc_custom_config
path('fastqc/*')
output:
path "*multiqc_report.html", emit: report
path "*_data" , emit: data
path "*_plots" , optional:true, emit: plots
path "*_data", emit: data
path "*_plots", optional: true, emit: plots
script:
// def custom_config = params.multiqc_config ? "--config $multiqc_custom_config" : ''
"""
multiqc -f $options.args .
multiqc -f $options.args $custom_config .
"""
}

8
tests/software/multiqc/main.nf
View file

@ -8,9 +8,13 @@ include { test_paired_end } from '../fastqc/main.nf' addParams( options: [ publ
workflow test_multiqc {
test_paired_end()
// test_paired_end.out.html.collect { it[1] }
// .join(test_paired_end.out.zip)
// .view()
input = [
[id: 'test'],
test_paired_end.out.html.join(test_paired_end.out.zip, by: 0).flatten().filter(java.nio.file.Path).toList()
test_paired_end.out.zip.collect { it[1] }.ifEmpty([])
]
MULTIQC(input)