nf-core_modules/modules/raxmlng/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } 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=1.0.3' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/raxml-ng:1.0.3--h32fcf60_0"
} else {
container "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
script:
"""
raxml-ng \\
$options.args \\
--msa $alignment \\
--threads $task.cpus \\
--prefix output
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(raxml-ng --version 2>&1) | sed 's/^.*RAxML-NG v. //; s/released.*\$//')
END_VERSIONS
"""
}