process RGI_MAIN { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::rgi=5.2.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rgi:5.2.1--pyha8f3691_2': 'quay.io/biocontainers/rgi:5.2.1--pyha8f3691_2' }" input: tuple val(meta), path(fasta) output: tuple val(meta), path("*.json"), emit: json tuple val(meta), path("*.txt") , 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}" """ rgi \\ main \\ $args \\ --num_threads $task.cpus \\ --output_file $prefix \\ --input_sequence $fasta cat <<-END_VERSIONS > versions.yml "${task.process}": rgi: \$(rgi main --version) END_VERSIONS """ }