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d9dfbe9d9d
* add pydamage module * remove TODOs * split module by subcommands * update version parsing * remove forgotten TODOs * update module names * remove old holistic module * Update modules/pydamage/analyze/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add keywords * simplify PR to analyze subcommand Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
40 lines
1.4 KiB
Text
40 lines
1.4 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 PYDAMAGE_ANALYZE {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${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:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::pydamage=0.62" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/pydamage:0.62--pyhdfd78af_0"
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} else {
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container "quay.io/biocontainers/pydamage:0.62--pyhdfd78af_0"
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}
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input:
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tuple val(meta), path(bam), path(bai)
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output:
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tuple val(meta), path("pydamage_results/pydamage_results.csv"), emit: csv
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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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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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pydamage \\
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analyze \\
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$options.args \\
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-p $task.cpus \\
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$bam
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echo \$(pydamage --version 2>&1) | sed -e 's/pydamage, version //g' > ${software}.version.txt
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"""
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}
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