mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
48 lines
1.8 KiB
Text
Executable file
48 lines
1.8 KiB
Text
Executable file
// 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=0.14.4" : 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("${prefix}.clades.tsv"), optional:true, emit: tsv_clades
|
|
path "*.version.txt" , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
prefix = options.suffix ? "${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
|
|
|
|
echo \$(nextclade --version 2>&1) > ${software}.version.txt
|
|
"""
|
|
}
|