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7b3315591a
* Remove def software line * Replace version with versions in emit statement * Fix default software names
40 lines
1.3 KiB
Text
40 lines
1.3 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process GFFREAD {
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tag "$gff"
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label 'process_low'
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publishDir "${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::gffread=0.12.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0"
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} else {
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container "quay.io/biocontainers/gffread:0.12.1--h8b12597_0"
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}
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input:
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path gff
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output:
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path "*.gtf" , emit: gtf
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${gff.baseName}${options.suffix}" : "${gff.baseName}"
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"""
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gffread \\
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$gff \\
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$options.args \\
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-o ${prefix}.gtf
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(gffread --version 2>&1)
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END_VERSIONS
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"""
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}
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