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52c541b080
* rebuild cooler cload. * update test file path of cload. * add pytest for cload * update to version.yml * update the test data path * Update tests/modules/cooler/cload/main.nf Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> * Update modules/cooler/cload/main.nf Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> * Update tests/config/test_data.config Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> * Update main.nf Remove a lonely curly bracket. * Update test.yml Updated with new workflows. * update the test files * merge the conflicts. * update the test.yml * update for change of cooler/dump Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
47 lines
1.6 KiB
Text
47 lines
1.6 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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process COOLER_CLOAD {
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tag "$meta.id"
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label 'process_high'
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publishDir "${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::cooler=0.8.11" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0"
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} else {
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container "quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0"
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}
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input:
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tuple val(meta), path(pairs), path(index)
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val cool_bin
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path chromsizes
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output:
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tuple val(meta), val(cool_bin), path("*.cool"), emit: cool
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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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def nproc = options.args.contains('pairix') || options.args.contains('tabix')? "--nproc ${task.cpus}" : ''
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"""
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cooler cload \\
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$options.args \\
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$nproc \\
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${chromsizes}:${cool_bin} \\
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$pairs \\
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${prefix}.${cool_bin}.cool
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(cooler --version 2>&1 | sed 's/cooler, version //')
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END_VERSIONS
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"""
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}
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