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2c43c39ccc
* Add pycoqc module * Adding pycoqc module tests * Update pycoqc wilth new functions.nf * Update tests to check for json report content
40 lines
1.2 KiB
Text
40 lines
1.2 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process PYCOQC {
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tag "$summary"
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
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conda (params.enable_conda ? "bioconda::pycoqc=2.5.2" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/pycoqc:2.5.2--py_0"
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} else {
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container "quay.io/biocontainers/pycoqc:2.5.2--py_0"
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}
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input:
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path summary
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output:
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path "*.html" , emit: html
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path "*.json" , emit: json
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path "*.version.txt", emit: version
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script:
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def software = getSoftwareName(task.process)
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"""
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pycoQC \\
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$options.args \\
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-f $summary \\
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-o pycoqc.html \\
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-j pycoqc.json
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echo \$(pycoQC --version 2>&1) | sed 's/^.*pycoQC v//; s/ .*\$//' > ${software}.version.txt
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"""
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}
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