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7b3315591a
* Remove def software line * Replace version with versions in emit statement * Fix default software names
48 lines
1.6 KiB
Text
48 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 TIDDIT_SV {
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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::tiddit=2.12.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/tiddit:2.12.1--py38h1773678_0"
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} else {
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container "quay.io/biocontainers/tiddit:2.12.1--py38h1773678_0"
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}
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input:
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tuple val(meta), path(bam)
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path fasta
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path fai
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output:
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tuple val(meta), path("*.vcf") , emit: vcf
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tuple val(meta), path("*.ploidy.tab") , emit: ploidy
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tuple val(meta), path("*.signals.tab"), emit: signals
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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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def reference = fasta == "dummy_file.txt" ? "--ref $fasta" : ""
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"""
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tiddit \\
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--sv \\
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$options.args \\
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--bam $bam \\
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$reference \\
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-o $prefix
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
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END_VERSIONS
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"""
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}
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