name: "muscle5_super5"
description: Muscle is a program for creating multiple alignments of amino acid or
  nucleotide sequences. This particular module uses the super5 algorithm for very
  big alignments. It can permutate the guide tree according to a set of flags.
keywords:
  - align
  - msa
  - multiple sequence alignment
tools:
  - muscle -super5:
      description: "Muscle v5 is a major re-write of MUSCLE based on new algorithms."
      homepage: "https://drive5.com/muscle5/"
      documentation: "https://drive5.com/muscle5/manual/"
      doi: "10.1101/2021.06.20.449169"
      licence: ["Public Domain"]
      identifier: ""
  - "pigz":
      description: "Parallel implementation of the gzip algorithm."
      homepage: "https://zlib.net/pigz/"
      documentation: "https://zlib.net/pigz/pigz.pdf"
      identifier: ""
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - fasta:
        type: file
        description: Input sequences for alignment must be in FASTA format
        pattern: "*.{fasta,fa,fna}"
  - - compress:
        type: boolean
        description: Flag representing whether the output MSA should be compressed.
          Set to true to enable/false to disable compression. Compression is done using
          pigz, and is multithreaded.
output:
  - alignment:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'test', single_end:false ]`
      - "*.aln{.gz,}":
          type: file
          description: Multiple sequence alignment produced in gzipped FASTA format. If
            '-perm all' is passed in ext.args, this will be multiple files per input!
          pattern: "*.{aln.gz}"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@alessiovignoli"
  - "@JoseEspinosa"
maintainers:
  - "@alessiovignoli"
  - "@JoseEspinosa"
  - "@lrauschning"
