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32ad1746d1
* Add vsearch sintax process * Add tests for vsearch sintax * Add vsearch sintax process * Add tests for vsearch sintax * Update format with prettier * Remove trailing whitespace Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
38 lines
1.1 KiB
Text
38 lines
1.1 KiB
Text
process VSEARCH_SINTAX {
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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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output:
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tuple val(meta), path('*.tsv') , optional: true, emit: tsv
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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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vsearch \\
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--sintax $queryfasta \\
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--db $db \\
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--threads $task.cpus \\
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$args \\
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--tabbedout ${prefix}.tsv
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cat <<-END_VERSIONS > versions.yml
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"${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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