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dcce431d51
* delete png and add stub * optional png file generation Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
50 lines
1.4 KiB
Text
50 lines
1.4 KiB
Text
process PEDDY {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::peddy=0.4.8" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/peddy:0.4.8--pyh5e36f6f_0' :
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'quay.io/biocontainers/peddy:0.4.8--pyh5e36f6f_0' }"
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input:
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tuple val(meta), path(vcf), path(vcf_tbi)
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path ped
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output:
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tuple val(meta), path("*.html") , emit: html
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tuple val(meta), path("*.csv") , emit: csv
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tuple val(meta), path("*.peddy.ped"), emit: ped
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tuple val(meta), path("*.png") , optional: true, emit: png
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path "versions.yml" , emit: versions
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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peddy \\
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$args \\
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--plot \\
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-p $task.cpus \\
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$vcf \\
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$ped
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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peddy: \$( peddy --version 2>&1 | sed 's/peddy, version //' )
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END_VERSIONS
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"""
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stub:
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"""
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filename=\$(basename $vcf)
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touch \$filename.ped_check.csv
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touch \$filename.vs.html
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touch \$filename.het_check.csv
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touch \$filename.sex_check.csv
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touch \$filename.peddy.ped
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touch \$filename.html
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touch versions.yml
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"""
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}
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