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https://github.com/MillironX/nf-core_modules.git
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906577873b
* New functions.nf * Convert code to create versions.yml * Update meta.yml * update output channel * Fix more meta.yml * Manually update remaining modules * remove superflous echo * Fix misformatted meta.yml files * Fix yaml, was list instead of dict * fix version for bcftools Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
50 lines
2.1 KiB
Text
50 lines
2.1 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 LAST_MAFCONVERT {
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tag "$meta.id"
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label 'process_high'
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publishDir "${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::last=1250' : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
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} else {
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container "quay.io/biocontainers/last:1250--h2e03b76_0"
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}
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input:
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tuple val(meta), path(maf)
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val(format)
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output:
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tuple val(meta), path("*.axt.gz"), optional:true, emit: axt_gz
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tuple val(meta), path("*.blast.gz"), optional:true, emit: blast_gz
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tuple val(meta), path("*.blasttab.gz"), optional:true, emit: blasttab_gz
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tuple val(meta), path("*.chain.gz"), optional:true, emit: chain_gz
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tuple val(meta), path("*.gff.gz"), optional:true, emit: gff_gz
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tuple val(meta), path("*.html.gz"), optional:true, emit: html_gz
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tuple val(meta), path("*.psl.gz"), optional:true, emit: psl_gz
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tuple val(meta), path("*.sam.gz"), optional:true, emit: sam_gz
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tuple val(meta), path("*.tab.gz"), optional:true, emit: tab_gz
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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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"""
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maf-convert $options.args $format $maf | gzip --no-name \\
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> ${prefix}.${format}.gz
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# maf-convert has no --version option but lastdb (part of the same package) has.
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(lastdb --version 2>&1 | sed 's/lastdb //')
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END_VERSIONS
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"""
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}
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