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61 lines
1.8 KiB
Text
61 lines
1.8 KiB
Text
process BCFTOOLS_ROH {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0':
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'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }"
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input:
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tuple val(meta), path(vcf), path(tbi)
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path af_file
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path genetic_map
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path regions_file
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path samples_file
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path targets_file
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output:
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tuple val(meta), path("*.roh"), emit: roh
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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 af_read = af_file ? "--AF-file ${af_file}" : ''
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def gen_map = genetic_map ? "--genetic-map ${genetic_map}" : ''
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def reg_file = regions_file ? "--regions-file ${regions_file}" : ''
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def samp_file = samples_file ? "--samples-file ${samples_file}" : ''
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def targ_file = targets_file ? "--targets-file ${targets_file}" : ''
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"""
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bcftools \\
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roh \\
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$args \\
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$af_read \\
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$gen_map \\
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$reg_file \\
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$samp_file \\
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$targ_file \\
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-o ${prefix}.roh \\
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$vcf
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}.roh
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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