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taxprofiler/modules/nf-core/multiqc/main.nf
2023-01-16 14:39:52 +01:00

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process MULTIQC {
label 'process_single'
conda "bioconda::multiqc=1.14"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
input:
path multiqc_files, stageAs: "?/*"
path(multiqc_config)
path(extra_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" : ''
def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
"""
multiqc \\
--force \\
$args \\
$config \\
$extra_config \\
.
cat <<-END_VERSIONS > versions.yml
"${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
"""
}