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7f7f6bc913
* Add hamronization/abricate * Update input pattern in meta.yml * Update location of hamronization test data * Apply suggestions from code review
43 lines
1.3 KiB
Text
43 lines
1.3 KiB
Text
process HAMRONIZATION_ABRICATE {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::hamronization=1.0.3" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/hamronization:1.0.3--py_0':
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'quay.io/biocontainers/hamronization:1.0.3--py_0' }"
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input:
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tuple val(meta), path(report)
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val(format)
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val(software_version)
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val(reference_db_version)
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output:
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tuple val(meta), path("*.json"), optional: true, emit: json
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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 ?: "${meta.id}"
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"""
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hamronize \\
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abricate \\
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${report} \\
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$args \\
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--format ${format} \\
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--analysis_software_version ${software_version} \\
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--reference_database_version ${reference_db_version} \\
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> ${prefix}.${format}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' )
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END_VERSIONS
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"""
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}
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