process ENTREZDIRECT_ESUMMARY { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/entrez-direct:16.2--he881be0_1': 'quay.io/biocontainers/entrez-direct:16.2--he881be0_1' }" input: tuple val(meta), val(uid), path(uids_file) val database output: tuple val(meta), path("*.xml"), emit: xml 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}" input = uids_file ? "-input ${uids_file}" : "-id ${uid}" if (!uid && !uids_file) error "No input. Valid input: an identifier or a .txt file with identifiers" if (uid && uids_file) error "Only one input is required: a single identifier or a .txt file with identifiers" """ esummary \\ $args \\ -db $database \\ $input > ${prefix}.xml cat <<-END_VERSIONS > versions.yml "${task.process}": esummary: \$(esummary -version) END_VERSIONS """ }