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e8b33e6eb1
* hifiasm copied from fastqc * hifiasm tests init from fastqc * meta.yml init; test.yml and main.nf for printing version * Add hifiasm version printing * Removed spaced on an empty line * Reverted hifiasm from main * Added genomecov scale module * Updated tagging * Removed extra module - began merging * Removed extra module tests * Updated genomecov to take a scale value * Updated line endings * Removed redundant test * Update tests/modules/bedtools/genomecov/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Added checking for existing -bg arg * Update modules/bedtools/genomecov/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/bedtools/genomecov/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk> Co-authored-by: Svyatoslav Sidorov <svet.sidorov@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
68 lines
2.2 KiB
Text
68 lines
2.2 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 BEDTOOLS_GENOMECOV {
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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::bedtools=2.30.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
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} else {
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container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
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}
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input:
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tuple val(meta), path(intervals), val(scale)
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path sizes
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val extension
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output:
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tuple val(meta), path("*.${extension}"), emit: genomecov
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def args_token = options.args.tokenize()
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def args = options.args
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args += (scale > 0 && scale != 1) ? " -scale $scale" : ""
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if (!args_token.contains('-bg') && (scale > 0 && scale != 1)) {
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args += " -bg"
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}
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if (intervals.name =~ /\.bam/) {
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"""
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bedtools \\
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genomecov \\
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-ibam $intervals \\
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$args \\
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> ${prefix}.${extension}
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
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END_VERSIONS
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"""
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} else {
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"""
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bedtools \\
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genomecov \\
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-i $intervals \\
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-g $sizes \\
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$args \\
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> ${prefix}.${extension}
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
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END_VERSIONS
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"""
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}
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}
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