process STAPHOPIASCCMEC { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::staphopia-sccmec=1.0.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/staphopia-sccmec:1.0.0--hdfd78af_0' : 'quay.io/biocontainers/staphopia-sccmec:1.0.0--hdfd78af_0' }" 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}" """ staphopia-sccmec --assembly $fasta $args > ${prefix}.tsv cat <<-END_VERSIONS > versions.yml "${task.process}": staphopiasccmec: \$(staphopia-sccmec --version 2>&1 | sed 's/^.*staphopia-sccmec //') END_VERSIONS """ }