mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 03:28:17 +00:00
34 lines
989 B
Text
34 lines
989 B
Text
process RAXMLNG {
|
|
label 'process_high'
|
|
|
|
conda (params.enable_conda ? 'bioconda::raxml-ng=1.0.3' : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/raxml-ng:1.0.3--h32fcf60_0' :
|
|
'quay.io/biocontainers/raxml-ng:1.0.3--h32fcf60_0' }"
|
|
|
|
input:
|
|
path alignment
|
|
|
|
output:
|
|
path "*.raxml.bestTree", emit: phylogeny
|
|
path "*.raxml.support" , optional:true, emit: phylogeny_bootstrapped
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
"""
|
|
raxml-ng \\
|
|
$args \\
|
|
--msa $alignment \\
|
|
--threads $task.cpus \\
|
|
--prefix output
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
raxmlng: \$(echo \$(raxml-ng --version 2>&1) | sed 's/^.*RAxML-NG v. //; s/released.*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|