nf-core_modules/modules/nextclade/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process NEXTCLADE {
tag "$meta.id"
label 'process_low'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::nextclade_js=0.14.4" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/nextclade_js:0.14.4--h9ee0642_0"
} else {
container "quay.io/biocontainers/nextclade_js:0.14.4--h9ee0642_0"
}
input:
tuple val(meta), path(fasta)
output:
tuple val(meta), path("${prefix}.csv") , emit: csv
tuple val(meta), path("${prefix}.json") , emit: json
tuple val(meta), path("${prefix}.tree.json") , emit: json_tree
tuple val(meta), path("${prefix}.tsv") , emit: tsv
tuple val(meta), path("${prefix}.clades.tsv"), optional:true, emit: tsv_clades
path "versions.yml" , emit: versions
script:
prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
nextclade \\
$options.args \\
--jobs $task.cpus \\
--input-fasta $fasta \\
--output-json ${prefix}.json \\
--output-csv ${prefix}.csv \\
--output-tsv ${prefix}.tsv \\
--output-tsv-clades-only ${prefix}.clades.tsv \\
--output-tree ${prefix}.tree.json
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(nextclade --version 2>&1)
END_VERSIONS
"""
}