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25943a4c23
* Add glnexus * Fix lint error * Refactor * Suggested changes Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
49 lines
1.7 KiB
Text
49 lines
1.7 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 GLNEXUS {
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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::glnexus=1.4.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/glnexus:1.4.1--h40d77a6_0"
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} else {
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container "quay.io/biocontainers/glnexus:1.4.1--h40d77a6_0"
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}
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input:
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tuple val(meta), path(gvcfs)
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output:
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tuple val(meta), path("*.bcf"), emit: bcf
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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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// Make list of GVCFs to merge
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def input = gvcfs.collect { it.toString() }
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def avail_mem = 3
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if (!task.memory) {
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log.info '[Glnexus] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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"""
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glnexus_cli \\
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--threads $task.cpus \\
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--mem-gbytes $avail_mem \\
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$options.args \\
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${input.join(' ')} \\
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> ${prefix}.bcf
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echo \$(glnexus_cli 2>&1) | head -n 1 | sed 's/^.*release //; s/ .*\$//' > ${software}.version.txt
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"""
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}
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