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f91abed951
* Export versions as explicit emission strings in addition to versions.yml for compatibility with hAMRonization * Update YML
43 lines
1.2 KiB
Text
43 lines
1.2 KiB
Text
process RGI_MAIN {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::rgi=5.2.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/rgi:5.2.1--pyha8f3691_2':
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'quay.io/biocontainers/rgi:5.2.1--pyha8f3691_2' }"
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input:
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tuple val(meta), path(fasta)
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output:
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tuple val(meta), path("*.json"), emit: json
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tuple val(meta), path("*.txt") , emit: tsv
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env VER , emit: tool_version
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env DBVER , emit: db_version
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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 ?: "${meta.id}"
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"""
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rgi \\
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main \\
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$args \\
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--num_threads $task.cpus \\
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--output_file $prefix \\
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--input_sequence $fasta
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VER=\$(rgi main --version)
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DBVER=\$(rgi database --version)
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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rgi: \$(echo \$VER)
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rgi-database: \$(echo \$DBVER)
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END_VERSIONS
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"""
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}
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