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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>
53 lines
2 KiB
Text
53 lines
2 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 PLASMIDID {
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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::plasmidid=1.6.5' : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container 'https://depot.galaxyproject.org/singularity/plasmidid:1.6.5--hdfd78af_0'
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} else {
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container 'quay.io/biocontainers/plasmidid:1.6.5--hdfd78af_0'
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}
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input:
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tuple val(meta), path(scaffold)
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path fasta
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output:
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tuple val(meta), path("${prefix}/*final_results.html"), emit: html
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tuple val(meta), path("${prefix}/*final_results.tab") , emit: tab
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tuple val(meta), path("${prefix}/images/") , emit: images
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tuple val(meta), path("${prefix}/logs/") , emit: logs
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tuple val(meta), path("${prefix}/data/") , emit: data
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tuple val(meta), path("${prefix}/database/") , emit: database
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tuple val(meta), path("${prefix}/fasta_files/") , emit: fasta_files
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tuple val(meta), path("${prefix}/kmer/") , emit: kmer
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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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prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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plasmidID \\
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-d $fasta \\
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-s $prefix \\
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-c $scaffold \\
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$options.args \\
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-o .
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mv NO_GROUP/$prefix ./$prefix
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(plasmidID --version 2>&1)
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END_VERSIONS
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"""
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}
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