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57 lines
2.6 KiB
Text
57 lines
2.6 KiB
Text
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process NCBIGENOMEDOWNLOAD {
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tag "$meta.id"
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label 'process_low'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::ncbi-genome-download=0.3.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/ncbi-genome-download:0.3.0--pyh864c0ab_1"
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} else {
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container "quay.io/biocontainers/ncbi-genome-download:0.3.0--pyh864c0ab_1"
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}
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input:
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val meta
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path accessions
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output:
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tuple val(meta), path("*_genomic.gbff.gz") , emit: gbk , optional: true
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tuple val(meta), path("*_genomic.fna.gz") , emit: fna , optional: true
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tuple val(meta), path("*_rm.out.gz") , emit: rm , optional: true
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tuple val(meta), path("*_feature_table.txt.gz") , emit: features, optional: true
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tuple val(meta), path("*_genomic.gff.gz") , emit: gff , optional: true
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tuple val(meta), path("*_protein.faa.gz") , emit: faa , optional: true
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tuple val(meta), path("*_protein.gpff.gz") , emit: gpff , optional: true
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tuple val(meta), path("*_wgsmaster.gbff.gz") , emit: wgs_gbk , optional: true
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tuple val(meta), path("*_cds_from_genomic.fna.gz"), emit: cds , optional: true
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tuple val(meta), path("*_rna.fna.gz") , emit: rna , optional: true
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tuple val(meta), path("*_rna_from_genomic.fna.gz"), emit: rna_fna , optional: true
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tuple val(meta), path("*_assembly_report.txt") , emit: report , optional: true
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tuple val(meta), path("*_assembly_stats.txt") , emit: stats , optional: true
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def accessions_opt = accessions ? "-A ${accessions}" : ""
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"""
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ncbi-genome-download \\
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$options.args \\
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$accessions_opt \\
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--output-folder ./ \\
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--flat-output
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$( ncbi-genome-download --version )
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END_VERSIONS
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"""
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}
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