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* 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 📦 NEW: Add galgal6 chr30 test data * 📦 NEW: Add bamtools module * 👌 IMPROVE: ignore test data * 👌 IMPROVE : add test bed files * 📦 NEW: Add gstama/merge module * 🐛 FIX: Change process label * 👌 IMPROVE: do not merge empty bed * 🐛 FIX: Change 0 lines files detection * 🐛 FIX: replace spaces by tab * 🐛 FIX: Remove tuple for report channel and add version output channel * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Update test * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Fix Typos * 👌 IMPROVE: Updates + clean code - Update to last versions.yml file - Better output channels - Update meta.yml * 👌 IMPROVE: Correct typo * 👌 IMPROVE: Remove included filelist creation and add an input channel * 🐛 FIX: Correct typo * 👌 IMPROVE: Add filelist file * 🐛 FIX: tama_merge.py emit a version number * Update modules/gstama/merge/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * 👌 IMPROVE: Update meta.yml * Update main.nf * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
46 lines
1.6 KiB
Text
46 lines
1.6 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 GSTAMA_MERGE {
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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::gs-tama=1.0.2" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gs-tama:1.0.2--hdfd78af_0"
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} else {
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container "quay.io/biocontainers/gs-tama:1.0.2--hdfd78af_0"
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}
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input:
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tuple val(meta), path(bed)
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path filelist
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output:
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tuple val(meta), path("*.bed") , emit: bed
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tuple val(meta), path("*_gene_report.txt") , emit: gene_report
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tuple val(meta), path("*_merge.txt") , emit: merge
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tuple val(meta), path("*_trans_report.txt"), emit: trans_report
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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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tama_merge.py \\
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-f $filelist \\
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-d merge_dup \\
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-p ${prefix} \\
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$options.args
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$( tama_merge.py -version | head -n1 )
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END_VERSIONS
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"""
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}
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