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374d81e0b3
* readcounter module for hmmcopy * Changed version number * Fix indentation * Update main.nf * Update modules/hmmcopy/readcounter/main.nf Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com> Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
42 lines
1.3 KiB
Text
42 lines
1.3 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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def VERSION = '0.1.1'
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process HMMCOPY_READCOUNTER {
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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::hmmcopy=0.1.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_5"
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} else {
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container "quay.io/biocontainers/hmmcopy:0.1.1--h2e03b76_5"
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}
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input:
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tuple val(meta), path(bam), path(bai)
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output:
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tuple val(meta), path("*.wig"), emit: wig
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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}" : "${meta.id}"
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"""
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readCounter \\
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$options.args \\
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${bam} > ${prefix}.wig
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo $VERSION)
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END_VERSIONS
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"""
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}
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