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38ffbfdb63
* bcf annotate ready2go * edited output name * fixed output * updated bcftools ver * changed contain output string * removed contain key entirely * fixed md5sum for test.yml * using match instead of find * bcftools/annotate refactored with complete test * rm trailing white space Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
42 lines
1.3 KiB
Text
42 lines
1.3 KiB
Text
process BCFTOOLS_ANNOTATE {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::bcftools=1.15" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bcftools:1.15--haf5b3da_0':
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'quay.io/biocontainers/bcftools:1.15--haf5b3da_0' }"
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input:
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tuple val(meta), path(input)
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output:
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tuple val(meta), path("*_annotated.vcf.gz"), optional:true , emit: vcf
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tuple val(meta), path("*_annotated.bcf") , optional:true , emit: bcf
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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 ?: "${meta.id}"
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def matcher = input ==~ /\S+\.*vcf\.\S*/
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def output_suffix = matcher ? "vcf.gz" : "bcf"
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def output_type_compressed = matcher ? "z" : "b"
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"""
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bcftools \\
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annotate \\
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$args \\
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--output ${prefix}_annotated.${output_suffix} \\
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--output-type $output_type_compressed \\
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--threads $task.cpus \\
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$input
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bcftools: \$( bcftools --version |& sed '1!d; s/^.*bcftools //' )
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END_VERSIONS
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"""
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}
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