mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
e937c7950a
* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
55 lines
2 KiB
Text
Executable file
55 lines
2 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)
|
|
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
|
|
"""
|
|
}
|