nf-core_modules/software/multiqc/main.nf
Harshil Patel dce27b8102
Update functions.nf to be more flexible for publishing by meta keys (#423)
* Update functions.nf

* Replace saveAs line in module main script

* Add spacing for ECLint
2021-04-09 17:23:56 +01:00

35 lines
1.2 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
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), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::multiqc=1.9" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/multiqc:1.9--pyh9f0ad1d_0"
} else {
container "quay.io/biocontainers/multiqc:1.9--pyh9f0ad1d_0"
}
input:
path multiqc_files
output:
path "*multiqc_report.html", emit: report
path "*_data" , emit: data
path "*_plots" , optional:true, emit: plots
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
"""
multiqc -f $options.args .
multiqc --version | sed -e "s/multiqc, version //g" > ${software}.version.txt
"""
}