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3cabc95d0e
* Updated the version of STAR in align and genomegenerate modules * Changes in test.yml * Changes in test.yml * Added module arriba * Changes in test configs * Added module Arriba for fusion detection * Fixed review comments * Added an output option for discarded fusions * Resolved some conflits * conflicts * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
47 lines
1.6 KiB
Text
47 lines
1.6 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 ARRIBA {
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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::arriba=2.1.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/arriba:2.1.0--h3198e80_1"
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} else {
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container "quay.io/biocontainers/arriba:2.1.0--h3198e80_1"
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}
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input:
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tuple val(meta), path(bam)
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path fasta
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path gtf
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output:
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tuple val(meta), path("*.fusions.tsv") , emit: fusions
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tuple val(meta), path("*.fusions.discarded.tsv"), emit: fusions_fail
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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 blacklist = (options.args.contains('-b')) ? '' : '-f blacklist'
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"""
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arriba \\
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-x $bam \\
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-a $fasta \\
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-g $gtf \\
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-o ${prefix}.fusions.tsv \\
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-O ${prefix}.fusions.discarded.tsv \\
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$blacklist \\
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$options.args
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echo \$(arriba -h | grep 'Version:' 2>&1) | sed 's/Version:\s//' > ${software}.version.txt
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"""
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}
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