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57 lines
2.0 KiB
Plaintext
57 lines
2.0 KiB
Plaintext
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 ATAQV_ATAQV {
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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::ataqv=1.2.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/ataqv:1.2.1--py39ha23c084_2"
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} else {
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container "quay.io/biocontainers/ataqv:1.2.1--py36hfdecbe1_2"
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}
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input:
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tuple val(meta), path(bam), path(bai), path(peak_file)
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val organism
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path tss_file
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path excl_regs_file
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path autosom_ref_file
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output:
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tuple val(meta), path("*.ataqv.json"), emit: json
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tuple val(meta), path("*.problems") , emit: problems, optional: true
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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 peak = peak_file ? "--peak-file $peak_file" : ''
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def tss = tss_file ? "--tss-file $tss_file" : ''
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def excl_regs = excl_regs_file ? "--excluded-region-file $excl_regs_file" : ''
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def autosom_ref = autosom_ref_file ? "--autosomal-reference-file $autosom_ref_file" : ''
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"""
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ataqv \\
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$options.args \\
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$peak \\
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$tss \\
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$excl_regs \\
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$autosom_ref \\
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--metrics-file "${prefix}.ataqv.json" \\
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--threads $task.cpus \\
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--name $prefix \\
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$organism \\
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$bam
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$( ataqv --version )
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END_VERSIONS
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"""
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}
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