process ABRICATE_SUMMARY { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1': 'quay.io/biocontainers/abricate:1.0.1--ha8f3691_1' }" input: tuple val(meta), path(reports) output: tuple val(meta), path("*.txt"), emit: report 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}" """ abricate \\ --summary \\ $reports > ${prefix}.txt cat <<-END_VERSIONS > versions.yml "${task.process}": abricate: \$(echo \$(abricate --version 2>&1) | sed 's/^.*abricate //' ) END_VERSIONS """ }