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https://github.com/MillironX/nf-core_modules.git
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bbf268c5d3
* 📦 NEW: First commit of pbccs module * 👌 IMPROVE: Remove option from command + rename output (ccs -> bam) * 👌 IMPROVE: Move .pbi output into report channel * 🐛FIX: Correct code after --rq option removal from command line module - module main.nf: Remove ramaining rq input channel - Test main.nf: Transfert rq into addParams - Test test.yml: Update md5sums * 🐛FIX: Repair additionnal option usage * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: CCS is run in parallel with --chunk option * 👌 IMPROVE: Add Pbindex in bam ouput channel * 👌 IMPROVE: Change label to process_low * 👌 IMPROVE: Define reports files names + add json version of txt report * 🐛 FIX: Add missing backslashes * 🐛 FIX: Add missing gz extension * 🐛 FIX: update ouput channel * 🐛 FIX: output file name * 👌 IMPROVE: .gitignore * 👌 IMPROVE: Update function.nf to last version * 👌 IMPROVE: Update saveAs in main.nf * 👌 IMPROVE: Add pbccs module * 🐛 FIX: Fix Broken test * 👌 IMPROVE: Update test_data.config * 🐛 FIX: Fix test * 👌 IMPROVE: Update path of test dataset files * 👌 IMPROVE: Remove useless index + Fix Typos * 📦 NEW: First commit of pbccs module * 👌 IMPROVE: Remove option from command + rename output (ccs -> bam) * 👌 IMPROVE: Move .pbi output into report channel * 🐛FIX: Correct code after --rq option removal from command line module - module main.nf: Remove ramaining rq input channel - Test main.nf: Transfert rq into addParams - Test test.yml: Update md5sums * 🐛FIX: Repair additionnal option usage * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: CCS is run in parallel with --chunk option * 👌 IMPROVE: Add Pbindex in bam ouput channel * 👌 IMPROVE: Change label to process_low * 👌 IMPROVE: Define reports files names + add json version of txt report * 🐛 FIX: Add missing backslashes * 🐛 FIX: Add missing gz extension * 🐛 FIX: update ouput channel * 🐛 FIX: output file name * 👌 IMPROVE: .gitignore * 👌 IMPROVE: Update function.nf to last version * 👌 IMPROVE: Update saveAs in main.nf * 👌 IMPROVE: Add pbccs module * 🐛 FIX: Fix Broken test * 👌 IMPROVE: Update test_data.config * 🐛 FIX: Fix test * 👌 IMPROVE: Update path of test dataset files * 👌 IMPROVE: Remove useless index + Fix Typos * 🐛 FIX: fill contains args * 👌 IMPROVE: One output => One Channel * 👌 IMPROVE: One input => One channel * 🐛 FIX: Update tests * 🐛 FIX: Remove TODOs from test.yaml * 👌 IMPROVE: Revert and keep bam and pbi together * 🐛 FIX: Remove old rq input from meta.yml * 👌 IMPROVE: Update test to match input channels Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
54 lines
2.1 KiB
Text
54 lines
2.1 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 PBCCS {
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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::pbccs=6.0.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/pbccs:6.0.0--h9ee0642_2"
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} else {
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container "quay.io/biocontainers/pbccs:6.0.0--h9ee0642_2"
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}
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input:
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tuple val(meta), path(bam), path(pbi)
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val chunk_num
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val chunk_on
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output:
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tuple val(meta), path("*.ccs.bam") , emit: bam
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tuple val(meta), path("*.ccs.bam.pbi") , emit: pbi
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tuple val(meta), path("*.ccs_report.txt" ) , emit: ccs_report_txt
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tuple val(meta), path("*.ccs_report.json" ) , emit: ccs_report_json
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tuple val(meta), path("*.zmw_metrics.json.gz"), emit: zmw_metrics
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tuple val(meta), 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}" : "${meta.id}"
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def ccs = bam.toString().replaceAll(/bam$/, '') + chunk_num + '.ccs.bam'
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def report_txt = bam.toString().replaceAll(/bam$/, '') + chunk_num + '.ccs_report.txt'
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def report_json = bam.toString().replaceAll(/bam$/, '') + chunk_num + '.ccs_report.json'
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def zmw_metrics = bam.toString().replaceAll(/bam$/, '') + chunk_num + '.zmw_metrics.json.gz'
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"""
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ccs \\
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$bam \\
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$ccs \\
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--report-file $report_txt \\
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--report-json $report_json \\
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--metrics-json $zmw_metrics \\
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--chunk $chunk_num/$chunk_on \\
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-j $task.cpus \\
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$options.args
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echo \$(ccs --version 2>&1) | grep -e 'commit' > ${software}.version.txt
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"""
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}
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