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38 lines
1.1 KiB
Text
38 lines
1.1 KiB
Text
process GUNC_RUN {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::gunc=1.0.5" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gunc:1.0.5--pyhdfd78af_0' :
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'quay.io/biocontainers/gunc:1.0.5--pyhdfd78af_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("*maxCSS_level.tsv") , emit: maxcss_level_tsv
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tuple val(meta), path("*all_levels.tsv") , optional: true, emit: all_levels_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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gunc \\
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run \\
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--input_fasta $fasta \\
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--db_file $db \\
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--threads $task.cpus \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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gunc: \$( gunc --version )
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END_VERSIONS
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"""
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}
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