process FASTTREE { label 'process_medium' conda (params.enable_conda ? "bioconda::fasttree=2.1.10" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fasttree:2.1.10--h516909a_4' : 'quay.io/biocontainers/fasttree:2.1.10--h516909a_4' }" input: path alignment output: path "*.tre", emit: phylogeny path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' """ fasttree \\ $args \\ -log fasttree_phylogeny.tre.log \\ -nt $alignment \\ > fasttree_phylogeny.tre cat <<-END_VERSIONS > versions.yml "${task.process}": fasttree: \$(fasttree -help 2>&1 | head -1 | sed 's/^FastTree \\([0-9\\.]*\\) .*\$/\\1/') END_VERSIONS """ }