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e0b7952b56
* add software/pairtools * create a branch for pairtools/select * fix the different output of conda and docker. * rmove the md5sum for gzip files. * Update software/pairtools/select/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * update test file and documentation. Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
41 lines
1.5 KiB
Text
41 lines
1.5 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 PAIRTOOLS_SELECT {
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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::pairtools=0.3.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5"
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} else {
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container "quay.io/biocontainers/pairtools:0.3.0--py37hb9c2fc3_5"
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}
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input:
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tuple val(meta), path(input)
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output:
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tuple val(meta), path("*.selected.pairs.gz") , emit: selected
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tuple val(meta), path("*.unselected.pairs.gz"), emit: unselected
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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}" : "${meta.id}"
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"""
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pairtools select \\
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"$options.args" \\
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-o ${prefix}.selected.pairs.gz \\
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--output-rest ${prefix}.unselected.pairs.gz \\
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${input}
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echo \$(pairtools --version 2>&1) | sed 's/pairtools.*version //' > ${software}.version.txt
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"""
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}
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