process NCBIGENOMEDOWNLOAD { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::ncbi-genome-download=0.3.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ncbi-genome-download:0.3.0--pyh864c0ab_1' : 'quay.io/biocontainers/ncbi-genome-download:0.3.0--pyh864c0ab_1' }" input: val meta path accessions output: tuple val(meta), path("*_genomic.gbff.gz") , emit: gbk , optional: true tuple val(meta), path("*_genomic.fna.gz") , emit: fna , optional: true tuple val(meta), path("*_rm.out.gz") , emit: rm , optional: true tuple val(meta), path("*_feature_table.txt.gz") , emit: features, optional: true tuple val(meta), path("*_genomic.gff.gz") , emit: gff , optional: true tuple val(meta), path("*_protein.faa.gz") , emit: faa , optional: true tuple val(meta), path("*_protein.gpff.gz") , emit: gpff , optional: true tuple val(meta), path("*_wgsmaster.gbff.gz") , emit: wgs_gbk , optional: true tuple val(meta), path("*_cds_from_genomic.fna.gz"), emit: cds , optional: true tuple val(meta), path("*_rna.fna.gz") , emit: rna , optional: true tuple val(meta), path("*_rna_from_genomic.fna.gz"), emit: rna_fna , optional: true tuple val(meta), path("*_assembly_report.txt") , emit: report , optional: true tuple val(meta), path("*_assembly_stats.txt") , emit: stats , optional: true 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}" def accessions_opt = accessions ? "-A ${accessions}" : "" """ ncbi-genome-download \\ $args \\ $accessions_opt \\ --output-folder ./ \\ --flat-output cat <<-END_VERSIONS > versions.yml "${task.process}": ncbigenomedownload: \$( ncbi-genome-download --version ) END_VERSIONS """ }