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f479d4fb8d
* files for learnreadorientationmodel initialised for first commit * finished scripts and yml files. test working locally but needs an f1r2 test data on nf-core before it can be submitted * updated test data location * versions file updated, test data added * updated versions file, edited test file * small formatting update to main.nf * Update main.nf * Update test_data.config * updated tests main.nf * Update test_data.config * Apply suggestions from code review * Update modules/gatk4/learnreadorientationmodel/main.nf * Update modules/gatk4/learnreadorientationmodel/meta.yml * fixed tests failing Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
44 lines
1.5 KiB
Text
44 lines
1.5 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 GATK4_LEARNREADORIENTATIONMODEL {
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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), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
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} else {
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container "quay.io/biocontainers/gatk4:4.2.0.0--0"
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}
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input:
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tuple val(meta), path(f1r2)
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output:
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tuple val(meta), path("*.tar.gz"), emit: artifactprior
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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}" : "${meta.id}"
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def inputs_list = []
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f1r2.each() { a -> inputs_list.add(" -I " + a) }
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"""
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gatk \\
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LearnReadOrientationModel \\
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${inputs_list.join(' ')} \\
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-O ${prefix}.tar.gz \\
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$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 \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
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END_VERSIONS
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"""
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}
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