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59ca7444cf
* adding plink module using nf-core tool [ci skip] * Restructures the project for plink/vcf (#1) * Add version string for plink * Create a plink/vcf module * small tweaks on main.nf and started to test [ci skip] * small changes on test args, local test with docker passed! * Update plink/vcf module listing * Update tag * fix tags as per linting guidelines * revert to the original state of tags * adding --threads to `main.nf` and `meta.yml` information Co-authored-by: Abhinav Sharma <abhi18av@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 } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process PLINK_VCF {
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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::plink=1.90b6.21" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/plink:1.90b6.21--h779adbc_1"
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} else {
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container "quay.io/biocontainers/plink:1.90b6.21--h779adbc_1"
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}
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input:
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tuple val(meta), path(vcf)
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output:
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tuple val(meta), path("*.bed"), emit: bed, optional: true
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tuple val(meta), path("*.bim"), emit: bim, optional: true
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tuple val(meta), path("*.fam"), emit: fam, optional: true
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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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"""
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plink \\
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--vcf ${vcf} \\
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$options.args \\
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--threads $task.cpus \\
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--out ${prefix}
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echo \$(plink --version 2>&1) | sed 's/^PLINK //' | sed 's/..-bit.*//'> ${software}.version.txt
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"""
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}
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