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79d38a306b
* 📦 NEW: Add isoseq3/refine module * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add parallelization * 🐛 FIX: Correct Typo * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The module accept one channel (primers moved into the first channel) * 👌 IMPROVE: Assign a value channel to primers input Improve workflow code readability * 👌 IMPROVE: Update to the version of templates * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Update test file * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Fill contains args * 📦 NEW: Add isoseq3/refine module * 👌 IMPROVE: Add parallelization * 🐛 FIX: Correct Typo * 👌 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 * 👌 IMPROVE: The module accept one channel (primers moved into the first channel) * 👌 IMPROVE: Assign a value channel to primers input Improve workflow code readability * 👌 IMPROVE: Update to the version of templates * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Update test file * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Fill contains args * 👌 IMPROVE: Add one channel per output file * 👌 IMPROVE: Minor updates * 👌 IMPROVE: Minors Update - Remove TODO from test.yml - Remove useless piece of code * 📦 NEW: Add isoseq3/refine module * 👌 IMPROVE: Add parallelization * 🐛 FIX: Correct Typo * 👌 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 * 👌 IMPROVE: The module accept one channel (primers moved into the first channel) * 👌 IMPROVE: Assign a value channel to primers input Improve workflow code readability * 👌 IMPROVE: Update to the version of templates * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Update test file * 👌 IMPROVE: Fill contains args * 📦 NEW: Add isoseq3/refine module * 👌 IMPROVE: Add parallelization * 🐛 FIX: Correct Typo * 👌 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 * 👌 IMPROVE: The module accept one channel (primers moved into the first channel) * 👌 IMPROVE: Assign a value channel to primers input Improve workflow code readability * 👌 IMPROVE: Update to the version of templates * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Update test file * 👌 IMPROVE: Add one channel per output file * 👌 IMPROVE: Minor updates * 👌 IMPROVE: Minors Update - Remove TODO from test.yml - Remove useless piece of code * 🐛 FIX: Remove unwanted files * 🐛 FIX: Protect \ * 🐛 FIX: Remove test files * Apply suggestions from code review * Apply suggestions from code review * Update tests/modules/isoseq3/refine/test.yml Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
49 lines
1.7 KiB
Text
49 lines
1.7 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 ISOSEQ3_REFINE {
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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::isoseq3=3.4.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/isoseq3:3.4.0--0"
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} else {
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container "quay.io/biocontainers/isoseq3:3.4.0--0"
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}
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input:
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tuple val(meta), path(bam)
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path primers
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output:
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tuple val(meta), path("*.bam") , emit: bam
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tuple val(meta), path("*.bam.pbi") , emit: pbi
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tuple val(meta), path("*.consensusreadset.xml"), emit: consensusreadset
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tuple val(meta), path("*.filter_summary.json") , emit: summary
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tuple val(meta), path("*.report.csv") , emit: 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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isoseq3 \\
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refine \\
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-j $task.cpus \\
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$options.args \\
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$bam \\
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$primers \\
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${prefix}.bam
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$( isoseq3 refine --version|sed 's/isoseq refine //'|sed 's/ (commit.\\+//' )
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END_VERSIONS
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"""
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}
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