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e9c57083a0
* Fix bug in gffread that would cause it to fail if the input has .gtf as extension * Update test.yml * Update meta file * Update main.nf * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
38 lines
1.2 KiB
Text
38 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 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 "*.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 ? "${gff.baseName}${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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echo \$(gffread --version 2>&1) > ${software}.version.txt
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"""
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}
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