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* Add IDR module * Add meta and implement main todos * Modifying idr tests * Update tests/config/test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/config/test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update main.nf * Update tests/config/test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update test with new file name Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
56 lines
1.9 KiB
Text
56 lines
1.9 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 IDR {
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tag "$prefix"
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label 'process_low'
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publishDir "${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), meta:[:], publish_by_meta:[]) }
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conda (params.enable_conda ? "bioconda::idr=2.0.4.2" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/idr:2.0.4.2--py39hcbe4a3b_5"
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} else {
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container "quay.io/biocontainers/idr:2.0.4.2--py38h9af456f_5"
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}
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input:
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path peaks
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val peak_type
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val prefix
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output:
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path "*idrValues.txt", emit: idr
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path "*log.txt" , emit: log
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path "*.png" , emit: png
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path "versions.yml" , emit: versions
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script:
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if (peaks.toList().size < 2) {
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log.error "[ERROR] idr needs at least two replicates only one provided."
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}
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def peak_types = ['narrowPeak', 'broadPeak', 'bed']
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if (!peak_types.contains(peak_type)) {
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log.error "[ERROR] Invalid option: '${peak_type}'. Valid options for 'peak_type': ${peak_types.join(', ')}."
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}
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def idr_vals = prefix ? "${prefix}.idrValues.txt" : "idrValues.txt"
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def log_file = prefix ? "${prefix}.log.txt" : "log.txt"
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"""
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idr \\
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--samples $peaks \\
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--input-file-type $peak_type \\
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--output-file $idr_vals \\
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--log-output-file $log_file \\
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--plot \\
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$options.args
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(idr --version 2>&1) | sed 's/^.*IDR //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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