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32 lines
960 B
Text
32 lines
960 B
Text
process HAPLOCHECK {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::haplocheck=1.3.3" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/haplocheck:1.3.3--h4a94de4_0':
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'quay.io/biocontainers/haplocheck:1.3.3--h4a94de4_0' }"
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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("*.txt"), emit: txt
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tuple val(meta), path("*.html"), emit: html
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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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haplocheck --raw --out $prefix $vcf
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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haplocheck: \$(echo \$(haplocheck --version 2>&1) | cut -f 2 -d " " )
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END_VERSIONS
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"""
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}
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