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https://github.com/MillironX/nf-core_modules.git
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daab0a77dd
* Update main.nf * Update meta.yml * Re-add logos as not staged in a way that works with MultiQC config files * Update main.nf * Remove now unnecessary input channel * Remove unused channel from tests * Update hAMRonization to 1.1.1 and add hAMRonization farGene * Fix hamronizatio ntests * Prettier * Fix fargene linting * Correct file * Fix fargene output * Apply suggestions from code review Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com> * Fix summarise tests * Prettier Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
43 lines
1.3 KiB
Text
43 lines
1.3 KiB
Text
process HAMRONIZATION_RGI {
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tag "$meta.id"
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label 'process_single'
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conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0':
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'quay.io/biocontainers/hamronization:1.1.1--pyhdfd78af_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 ?: "${meta.id}"
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"""
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hamronize \\
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rgi \\
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${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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--input_file_name ${prefix} \\
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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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