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e27553b989
* Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * feat: add megahit module, currently decompressed output * Update main.nf * Update tests/modules/megahit/test.yml Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * feat: compress all outputs, remove md5sums due to gz stochasicity * fix: wrong conda channel for pigz * fix: broken singleend tests and update meta.yml * Missed one * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fix: pigz formatting * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * Add dedup (tests and version not working) * Fix dedup and tests Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
47 lines
1.6 KiB
Text
47 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 DEDUP {
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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::dedup=0.12.8" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/dedup:0.12.8--hdfd78af_1"
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} else {
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container "quay.io/biocontainers/dedup:0.12.8--hdfd78af_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("*_rmdup.bam"), emit: bam // _rmdup is hardcoded output from dedup
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tuple val(meta), path("*.json") , emit: json
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tuple val(meta), path("*.hist") , emit: hist
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tuple val(meta), path("*log") , emit: log
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path "versions.yml" , emit: versions
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script:
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prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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dedup \\
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-Xmx${task.memory.toGiga()}g \\
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-i $bam \\
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-o . \\
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$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 \$(dedup --version 2>&1) | tail -n 1 | sed 's/.* v//')
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END_VERSIONS
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"""
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}
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