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de0d57a562
* implement plink2/score module * fix test yml * fix typo :( * set cpu * set mem * fix input process input block * fix tests Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
39 lines
1.1 KiB
Text
39 lines
1.1 KiB
Text
process PLINK2_SCORE {
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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(pgen), path(psam), path(pvar)
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path(scorefile)
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output:
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tuple val(meta), path("*.sscore"), emit: score
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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() // plink is greedy
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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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--pfile ${pgen.baseName} vzs \\
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--score ${scorefile} \\
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$args \\
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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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