nf-core_modules/modules/bcftools/isec/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
options = initOptions(params.options)
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process BCFTOOLS_ISEC {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
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} else {
container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
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}
input:
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tuple val(meta), path(vcfs), path(tbis)
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output:
tuple val(meta), path("${prefix}"), emit: results
path "versions.yml" , emit: versions
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script:
prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
bcftools isec \\
$options.args \\
-p $prefix \\
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*.vcf.gz
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
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"""
}