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 """ }