nf-core_modules/software/nextclade/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } 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=0.14.2" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/nextclade_js:0.14.2--h9ee0642_0"
} else {
container "quay.io/biocontainers/nextclade_js:0.14.2--h9ee0642_0"
}
input:
tuple val(meta), path(fasta)
val output_format
output:
tuple val(meta), path("${prefix}.csv") , optional:true, emit: csv
tuple val(meta), path("${prefix}.json") , optional:true, emit: json
tuple val(meta), path("${prefix}.tree.json") , optional:true, emit: json_tree
tuple val(meta), path("${prefix}.tsv") , optional:true, emit: tsv
tuple val(meta), path("${prefix}.clades.tsv"), optional:true, emit: tsv_clades
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def format = output_format
if (!(format in ['json', 'csv', 'tsv', 'tree', 'tsv-clades-only'])) {
format = 'json'
}
def extension = format
if (format in ['tsv-clades-only']) {
extension = '.clades.tsv'
} else if (format in ['tree']) {
extension = 'tree.json'
}
"""
nextclade \\
$options.args \\
--jobs $task.cpus \\
--input-fasta $fasta \\
--output-${format} ${prefix}.${extension}
echo \$(nextclade --version 2>&1) > ${software}.version.txt
"""
}