process MLST { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::mlst=2.19.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mlst:2.19.0--hdfd78af_1' : 'quay.io/biocontainers/mlst:2.19.0--hdfd78af_1' }" input: tuple val(meta), path(fasta) output: tuple val(meta), path("*.tsv"), emit: tsv path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ mlst \\ --threads $task.cpus \\ $fasta \\ > ${prefix}.tsv cat <<-END_VERSIONS > versions.yml "${task.process}": mlst: \$( echo \$(mlst --version 2>&1) | sed 's/mlst //' ) END_VERSIONS """ }