mirror of
https://github.com/MillironX/nf-core_modules.git
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e751e5040a
* Bump software versions for viralrecon modules * Remove custom params.save_unaligned from bowtie2_align * Unify samtools modules and error if input and output names are the same * Fix ALL the tests
41 lines
1.3 KiB
Text
41 lines
1.3 KiB
Text
process BCFTOOLS_VIEW {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
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'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
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input:
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tuple val(meta), path(vcf), path(index)
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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("*.gz") , emit: vcf
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path "versions.yml" , emit: versions
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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 view \\
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--output ${prefix}.vcf.gz \\
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${regions_file} \\
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${targets_file} \\
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${samples_file} \\
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$args \\
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--threads $task.cpus \\
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${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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