nf-core_modules/modules/ncbigenomedownload/main.nf
2022-02-04 09:53:32 +01:00

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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
"""
}