nf-core_modules/modules/multiqc/main.nf
Matthias De Smet e5f8924fab
Update modules/multiqc/main.nf
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
2022-06-08 14:41:10 +02:00

49 lines
1.3 KiB
Text

process MULTIQC {
label 'process_medium'
conda (params.enable_conda ? 'bioconda::multiqc=1.12' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' :
'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }"
input:
path multiqc_files, stageAs: "?/*"
tuple path(multiqc_config), path(multiqc_logo)
output:
path "*multiqc_report.html", emit: report
path "*_data" , emit: data
path "*_plots" , optional:true, emit: plots
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def config = multiqc_config ? "--config $multiqc_config" : ''
"""
multiqc \\
--force \\
$config \\
$args \\
.
cat <<-END_VERSIONS > versions.yml
"${task.process}":
multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
END_VERSIONS
"""
stub:
"""
touch multiqc_data
touch multiqc_plots
touch multiqc_report.html
cat <<-END_VERSIONS > versions.yml
"${task.process}":
multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
END_VERSIONS
"""
}