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

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process NEXTCLADE_DATASETGET {
tag "$dataset"
label 'process_low'
conda (params.enable_conda ? "bioconda::nextclade=1.10.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/nextclade:1.10.2--h9ee0642_0' :
'quay.io/biocontainers/nextclade:1.10.2--h9ee0642_0' }"
input:
val dataset
val reference
val tag
output:
path "$prefix" , emit: dataset
path "versions.yml", emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${dataset}"
def fasta = reference ? "--reference ${reference}" : ''
def version = tag ? "--tag ${tag}" : ''
"""
nextclade \\
dataset \\
get \\
$args \\
--name $dataset \\
$fasta \\
$version \\
--output-dir $prefix
cat <<-END_VERSIONS > versions.yml
"${task.process}":
nextclade: \$(nextclade --version 2>&1)
END_VERSIONS
"""
}