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bcf2681b03
* 👌 IMPROVE: Add some pacbio test files * 📦 NEW: Add pbbam/pbmerge module * 🐛 FIX: Add optional arguments to command line * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Update test data config and test script * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Add some pacbio test files * 📦 NEW: Add pbbam/pbmerge module * 🐛 FIX: Add optional arguments to command line * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Update test data config and test script * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Update and clean code * 🐛 FIX: Update module path in test * 🐛 FIX: Add missing () + correct module path in test * 👌 IMPROVE: Update pbmerge from version 1.6.0 to 1.7.0 * 👌 IMPROVE: Change output filename suffix for something more generic * 🐛 Update test.yml * Apply suggestions from code review * Update tests/modules/pbbam/pbmerge/test.yml * Update tests/modules/pbbam/pbmerge/main.nf Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
42 lines
1.3 KiB
Text
42 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 PBBAM_PBMERGE {
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tag "$meta.id"
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label 'process_low'
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publishDir "${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:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::pbbam=1.7.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/pbbam:1.7.0--h058f120_1"
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} else {
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container "quay.io/biocontainers/pbbam:1.7.0--h058f120_1"
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}
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input:
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tuple val(meta), path(bam)
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output:
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tuple val(meta), path("*.bam"), emit: bam
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tuple val(meta), path("*.pbi"), emit: pbi
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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pbmerge \\
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-o ${prefix}.bam \\
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$options.args \\
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*.bam
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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pbbam/pbmerge: \$( pbmerge --version|sed 's/pbmerge //' )
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END_VERSIONS
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"""
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}
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