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 """ }