mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
67 lines
2.7 KiB
Text
67 lines
2.7 KiB
Text
process VSEARCH_USEARCHGLOBAL {
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tag "${meta.id}"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::vsearch=2.21.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/vsearch:2.21.1--h95f258a_0':
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'quay.io/biocontainers/vsearch:2.21.1--h95f258a_0' }"
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input:
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tuple val(meta), path(queryfasta)
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path db
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val idcutoff
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val outoption
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val user_columns
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output:
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tuple val(meta), path('*.aln') , optional: true, emit: aln
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tuple val(meta), path('*.biom') , optional: true, emit: biom
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tuple val(meta), path('*.lca') , optional: true, emit: lca
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tuple val(meta), path('*.mothur') , optional: true, emit: mothur
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tuple val(meta), path('*.otu') , optional: true, emit: otu
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tuple val(meta), path('*.sam') , optional: true, emit: sam
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tuple val(meta), path('*.tsv') , optional: true, emit: tsv
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tuple val(meta), path('*.txt') , optional: true, emit: txt
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tuple val(meta), path('*.uc') , optional: true, emit: uc
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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 columns = user_columns ? "--userfields ${user_columns}" : ''
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switch ( outoption ) {
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case "alnout": outfmt = "--alnout"; out_ext = 'aln'; break
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case "biomout": outfmt = "--biomout"; out_ext = 'biom'; break
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case "blast6out": outfmt = "--blast6out"; out_ext = 'txt'; break
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case "mothur_shared_out": outfmt = "--mothur_shared_out"; out_ext = 'mothur'; break
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case "otutabout": outfmt = "--otutabout"; out_ext = 'otu'; break
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case "samout": outfmt = "--samout"; out_ext = 'sam'; break
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case "uc": outfmt = "--uc"; out_ext = 'uc'; break
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case "userout": outfmt = "--userout"; out_ext = 'tsv'; break
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case "lcaout": outfmt = "--lcaout"; out_ext = 'lca'; break
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default:
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outfmt = "--alnout";
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out_ext = 'aln';
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log.warn("Unknown output file format provided (${outoption}): selecting pairwise alignments (alnout)");
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break
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}
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"""
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vsearch \\
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--usearch_global $queryfasta \\
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--db $db \\
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--id $idcutoff \\
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--threads $task.cpus \\
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$args \\
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${columns} \\
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${outfmt} ${prefix}.${out_ext}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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vsearch: \$(vsearch --version 2>&1 | head -n 1 | sed 's/vsearch //g' | sed 's/,.*//g' | sed 's/^v//' | sed 's/_.*//')
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END_VERSIONS
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"""
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}
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