nf-core_modules/modules/pycoqc/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process PYCOQC {
tag "$summary"
label 'process_medium'
publishDir "${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::pycoqc=2.5.2" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/pycoqc:2.5.2--py_0"
} else {
container "quay.io/biocontainers/pycoqc:2.5.2--py_0"
}
input:
path summary
output:
path "*.html" , emit: html
path "*.json" , emit: json
path "versions.yml" , emit: versions
script:
"""
pycoQC \\
$options.args \\
-f $summary \\
-o pycoqc.html \\
-j pycoqc.json
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(pycoQC --version 2>&1 | sed 's/^.*pycoQC v//; s/ .*\$//')
END_VERSIONS
"""
}