process MUSCLE { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::muscle=3.8.1551" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/muscle:3.8.1551--h7d875b9_6' : 'quay.io/biocontainers/muscle:3.8.1551--h7d875b9_6' }" input: tuple val(meta), path(fasta) output: tuple val(meta), path("*.afa") , optional: true, emit: aligned_fasta tuple val(meta), path("*.phyi"), optional: true, emit: phyi tuple val(meta), path("*.phys"), optional: true, emit: phys tuple val(meta), path("*.clw") , optional: true, emit: clustalw tuple val(meta), path("*.html"), optional: true, emit: html tuple val(meta), path("*.msf") , optional: true, emit: msf tuple val(meta), path("*.tree"), optional: true, emit: tree path "*.log" , emit: log path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def fasta_out = args.contains('-fasta') ? "-fastaout ${prefix}_muscle_msa.afa" : '' def clw_out = args.contains('-clw') ? "-clwout ${prefix}_muscle_msa.clw" : '' def msf_out = args.contains('-msf') ? "-msfout ${prefix}_muscle_msa.msf" : '' def phys_out = args.contains('-phys') ? "-physout ${prefix}_muscle_msa.phys" : '' def phyi_out = args.contains('-phyi') ? "-phyiout ${prefix}_muscle_msa.phyi" : '' def html_out = args.contains('-html') ? "-htmlout ${prefix}_muscle_msa.html" : '' def tree_out = args.contains('-maketree') ? "-out ${prefix}_muscle_msa.tree" : '' """ muscle \\ $args \\ -in $fasta \\ $fasta_out \\ $clw_out \\ $msf_out \\ $phys_out \\ $phyi_out \\ $html_out \\ $tree_out \\ -loga muscle_msa.log cat <<-END_VERSIONS > versions.yml "${task.process}": muscle: \$(muscle -version | sed 's/^MUSCLE v//; s/by.*\$//') END_VERSIONS """ }