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https://github.com/MillironX/nf-core_modules.git
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682f789f93
* Bump tool versions for modules required in viralrecon * Fix all the tests * Fix Prettier lint * Remove empty md5sums
43 lines
1.3 KiB
Text
43 lines
1.3 KiB
Text
process BCFTOOLS_QUERY {
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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 regions
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path targets
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path samples
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output:
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tuple val(meta), path("*.txt"), emit: txt
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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 regions_file = regions ? "--regions-file ${regions}" : ""
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def targets_file = targets ? "--targets-file ${targets}" : ""
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def samples_file = samples ? "--samples-file ${samples}" : ""
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"""
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bcftools query \\
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--output ${prefix}.txt \\
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$regions_file \\
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$targets_file \\
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$samples_file \\
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$args \\
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$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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}
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