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42 lines
1.2 KiB
Text
42 lines
1.2 KiB
Text
process DIAMOND_BLASTX {
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tag "$meta.id"
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label 'process_medium'
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// Dimaond is limited to v2.0.9 because there is not a
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// singularity version higher than this at the current time.
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conda (params.enable_conda ? "bioconda::diamond=2.0.9" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0' :
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'quay.io/biocontainers/diamond:2.0.9--hdcc8f71_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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output:
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tuple val(meta), path('*.txt'), emit: txt
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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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"""
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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 $fasta \\
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$args \\
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--out ${prefix}.txt
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cat <<-END_VERSIONS > versions.yml
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"${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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