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e937c7950a
* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
55 lines
1.8 KiB
Text
55 lines
1.8 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 STRINGTIE {
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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::stringtie=2.1.4" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/stringtie:2.1.4--h7e0af3c_0"
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} else {
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container "quay.io/biocontainers/stringtie:2.1.4--h7e0af3c_0"
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}
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input:
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tuple val(meta), path(bam)
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path gtf
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output:
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tuple val(meta), path("*.coverage.gtf") , emit: coverage_gtf
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tuple val(meta), path("*.transcripts.gtf"), emit: transcript_gtf
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tuple val(meta), path("*.abundance.txt") , emit: abundance
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tuple val(meta), path("*.ballgown") , emit: ballgown
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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}" : "${meta.id}"
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def strandedness = ''
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if (meta.strandedness == 'forward') {
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strandedness = '--fr'
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} else if (meta.strandedness == 'reverse') {
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strandedness = '--rf'
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}
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"""
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stringtie \\
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$bam \\
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$strandedness \\
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-G $gtf \\
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-o ${prefix}.transcripts.gtf \\
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-A ${prefix}.gene.abundance.txt \\
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-C ${prefix}.coverage.gtf \\
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-b ${prefix}.ballgown \\
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$options.args
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stringtie --version > ${software}.version.txt
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"""
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}
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