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3d720a24fd
* Add allelecount module * Add bed file input * Added bai file * Changed conda version * Update main.nf * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Add allelecount module * Add bed file input * Added bai file * Changed conda version * Update main.nf * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Remove newline * Fix pytest_software.yml * Update pytest_software.yml Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
41 lines
1.3 KiB
Text
41 lines
1.3 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process ALLELECOUNTER {
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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), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::cancerit-allelecount=4.2.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/cancerit-allelecount:4.2.1--h3ecb661_0"
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} else {
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container "quay.io/biocontainers/cancerit-allelecount:4.2.1--h3ecb661_0"
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}
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input:
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tuple val(meta), path(bam), path(bai)
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path loci
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output:
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tuple val(meta), path("*.alleleCount"), emit: allelecount
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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alleleCounter \\
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$options.args \\
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-l $loci \\
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-b $bam \\
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-o ${prefix}.alleleCount
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alleleCounter --version > ${software}.version.txt
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"""
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}
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