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69 lines
2.3 KiB
Plaintext
69 lines
2.3 KiB
Plaintext
process DIAMOND_BLASTX {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' :
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'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }"
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input:
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tuple val(meta), path(fasta)
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path db
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val out_ext
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val blast_columns
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output:
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tuple val(meta), path('*.blast'), optional: true, emit: blast
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tuple val(meta), path('*.xml') , optional: true, emit: xml
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tuple val(meta), path('*.txt') , optional: true, emit: txt
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tuple val(meta), path('*.daa') , optional: true, emit: daa
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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('*.paf') , optional: true, emit: paf
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tuple val(meta), path("*.log") , emit: log
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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 ?: "${meta.id}"
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def columns = blast_columns ? "${blast_columns}" : ''
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switch ( out_ext ) {
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case "blast": outfmt = 0; break
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case "xml": outfmt = 5; break
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case "txt": outfmt = 6; break
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case "daa": outfmt = 100; break
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case "sam": outfmt = 101; break
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case "tsv": outfmt = 102; break
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case "paf": outfmt = 103; break
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default:
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outfmt = '6';
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out_ext = 'txt';
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log.warn("Unknown output file format provided (${out_ext}): selecting DIAMOND default of tabular BLAST output (txt)");
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break
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}
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"""
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DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'`
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diamond \\
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blastx \\
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--threads $task.cpus \\
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--db \$DB \\
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--query $fasta \\
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--outfmt ${outfmt} ${columns} \\
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$args \\
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--out ${prefix}.${out_ext} \\
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--log
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mv diamond.log ${prefix}.log
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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diamond: \$(diamond --version 2>&1 | tail -n 1 | sed 's/^diamond version //')
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END_VERSIONS
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"""
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}
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