mirror of
https://github.com/MillironX/nf-core_modules.git
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bb90e4fb78
* Remove customisation from bcftools modules * Add save_mpileup option to bcftools/mpileup * Remove params.save_mpileup from ivar/consensus * Update meta.ymls
33 lines
993 B
Text
33 lines
993 B
Text
process BCFTOOLS_CONSENSUS {
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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(tbi), path(fasta)
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output:
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tuple val(meta), path('*.fa'), emit: fasta
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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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"""
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cat $fasta \\
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| bcftools \\
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consensus \\
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$vcf \\
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$args \\
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> ${prefix}.fa
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cat <<-END_VERSIONS > versions.yml
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"${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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