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https://github.com/MillironX/nf-core_modules.git
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cde1d827f9
* Fix kallisto index tests * Fix nanoplot * Fix kallistobustools * Fix pairix * Fix plasmidid * Fix pbccs * Fix raxmlng * Fix prokka * Fix shovill * Fix typo * Deleted workflow by mistake added again
57 lines
2.3 KiB
Text
57 lines
2.3 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 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("versions.yml" ) , 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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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(ccs --version 2>&1) | grep 'ccs' | sed 's/^.*ccs //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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