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8e5eaf1fa4
* update plink2/vcf to output zstandard compressed data automatically * update meta * set plink CPU and memory usage Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
40 lines
1.2 KiB
Text
40 lines
1.2 KiB
Text
process PLINK2_VCF {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1' :
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'quay.io/biocontainers/plink2:2.00a2.3--h712d239_1' }"
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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("*.pgen") , emit: pgen
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tuple val(meta), path("*.psam") , emit: psam
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tuple val(meta), path("*.pvar.zst"), emit: pvar
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def mem_mb = task.memory.toMega()
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"""
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plink2 \\
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--threads $task.cpus \\
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--memory $mem_mb \\
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$args \\
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--vcf $vcf \\
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--make-pgen vzs \\
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--out ${prefix}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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plink2: \$(plink2 --version 2>&1 | sed 's/^PLINK v//; s/ 64.*\$//' )
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END_VERSIONS
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"""
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}
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