def VERSION = '2.3.2' // Version information not provided by tool on CLI process RAPIDNJ { label 'process_medium' conda (params.enable_conda ? "bioconda::rapidnj=2.3.2 conda-forge::biopython=1.78" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0' : 'quay.io/biocontainers/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0' }" input: path alignment output: path "*.sth" , emit: stockholm_alignment path "*.tre" , emit: phylogeny path "versions.yml", emit: versions script: def args = task.ext.args ?: '' """ python \\ -c 'from Bio import SeqIO; SeqIO.convert("$alignment", "fasta", "alignment.sth", "stockholm")' rapidnj \\ alignment.sth \\ $args \\ -i sth \\ -c $task.cpus \\ -x rapidnj_phylogeny.tre cat <<-END_VERSIONS > versions.yml "${task.process}": rapidnj: $VERSION biopython: \$(python -c "import Bio; print(Bio.__version__)") END_VERSIONS """ }