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78e2e76b24
* hmmcopy/mapCounter * update test * Remove bam tag * Remove /tmp/ path from test.yml * Update modules/hmmcopy/mapcounter/meta.yml Incorporate formatting changes Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/hmmcopy/mapcounter/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update tests/modules/hmmcopy/mapcounter/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * ichorCNA run * Add panel of normals code * Try and fix tests * Edit string detection in tests * Fix linting issues * Just failing END_VERSIONS * Fixed versions.yml * Added DOI * Optional name for file * Add when command * Updated when * Update modules/ichorcna/createpon/main.nf Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
50 lines
1.5 KiB
Text
50 lines
1.5 KiB
Text
def VERSION = '0.3.2' // Version information not provided by tool on CLI
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process ICHORCNA_RUN {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::r-ichorcna=0.3.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/r-ichorcna:0.3.2--r41hdfd78af_0' :
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'quay.io/biocontainers/r-ichorcna:0.3.2--r41hdfd78af_0' }"
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input:
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tuple val(meta), path(wig)
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path gc_wig
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path map_wig
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path panel_of_normals
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path centromere
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output:
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tuple val(meta), path("*.cna.seg") , emit: cna_seg
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tuple val(meta), path("*.params.txt") , emit: ichorcna_params
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path "**/*genomeWide.pdf" , emit: genome_plot
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def pon = panel_of_normals ? "--normalPanel ${panel_of_normals}" : ''
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def centro = centromere ? "--centromere ${centromere}" : ''
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"""
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runIchorCNA.R --id ${prefix} \\
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$args \\
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--WIG ${wig} \\
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--id ${meta.id} \\
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--gcWig ${gc_wig} \\
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--mapWig ${map_wig} \\
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${pon} \\
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${centro} \\
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--outDir .
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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ichorcna: $VERSION
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END_VERSIONS
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"""
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}
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