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https://github.com/MillironX/nf-core_modules.git
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39 lines
1.1 KiB
Text
39 lines
1.1 KiB
Text
process PLINK_VCF {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::plink=1.90b6.21" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/plink:1.90b6.21--h779adbc_1' :
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'quay.io/biocontainers/plink:1.90b6.21--h779adbc_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("*.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 "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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"""
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plink \\
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--vcf ${vcf} \\
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$args \\
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--threads $task.cpus \\
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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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plink: \$(echo \$(plink --version 2>&1) | sed 's/^PLINK v//' | sed 's/..-bit.*//' )
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END_VERSIONS
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"""
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}
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