mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-26 23:43:19 -05:00
6a31737cb8
* raxml-ng is compute intensive - upgrade process label to high * ensure raxmlng uses --all when bootstrapping * remove block that should be taken of by the options passed in * update tests
39 lines
1.3 KiB
Text
39 lines
1.3 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process RAXMLNG {
|
|
label 'process_high'
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
|
|
|
|
conda (params.enable_conda ? "bioconda::raxml-ng=1.0.2" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/raxml-ng:1.0.2--h7447c1b_0"
|
|
} else {
|
|
container "quay.io/biocontainers/raxml-ng:1.0.2--h7447c1b_0"
|
|
}
|
|
|
|
input:
|
|
path alignment
|
|
|
|
output:
|
|
path "*.raxml.bestTree", emit: phylogeny
|
|
path "*.raxml.support" , optional:true, emit: phylogeny_bootstrapped
|
|
path "*.version.txt" , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
"""
|
|
raxml-ng \\
|
|
$options.args \\
|
|
--msa $alignment \\
|
|
--threads $task.cpus \\
|
|
--prefix output
|
|
|
|
echo \$(raxml-ng --version 2>&1) | sed 's/^.*RAxML-NG v. //; s/released.*\$//' > ${software}.version.txt
|
|
"""
|
|
}
|