process HAMRONIZATION_AMRFINDERPLUS { tag "$meta.id" label 'process_single' conda (params.enable_conda ? "bioconda::hamronization=1.1.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0': 'quay.io/biocontainers/hamronization:1.1.1--pyhdfd78af_0' }" input: tuple val(meta), path(report) val(format) val(software_version) val(reference_db_version) output: tuple val(meta), path("*.json") , optional: true, emit: json tuple val(meta), path("*.tsv") , optional: true, emit: tsv path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ hamronize \\ amrfinderplus \\ ${report} \\ $args \\ --format ${format} \\ --analysis_software_version ${software_version} \\ --reference_database_version ${reference_db_version} \\ --input_file_name ${prefix} \\ > ${prefix}.${format} cat <<-END_VERSIONS > versions.yml "${task.process}": hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' ) END_VERSIONS """ }