nf-core_modules/modules/muscle/meta.yml

name: muscle
description: MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options are provided that give you the choice of optimizing accuracy, speed, or some compromise between the two
keywords:
  - msa
  - multiple sequence alignment
tools:
  - muscle:
    description: MUSCLE is a multiple sequence alignment tool with high accuracy and throughput
    homepage: https://www.drive5.com/muscle
    documentation: http://www.drive5.com/muscle/muscle.html#_Toc81224840
    doi: "https://pubmed.ncbi.nlm.nih.gov/15034147/"
    licence: ["http://www.drive5.com/muscle/manual/license.html"]
input:
  - fasta:
      type: file
      description: Input sequences for alignment must be in FASTA format
      pattern: "*.{fasta,fa,fna}"
output:
  - aligned_fasta:
      type: file
      description: Multiple sequence alignment produced in FASTA format
      pattern: "*.{afa}"
  - msf:
      type: file
      description: GCG Multiple Sequence File (MSF) alignment format (similar to CLUSTALW)
      pattern: "*.{msf}"
  - clustalw:
      type: file
      description: Multiple sequence alignment produced in ClustalW format without base/residue numbering
      pattern: "*.{clw}"
  - phyi:
      type: file
      description: Multiple sequence alignment produced in PHYLIP interleaved format
      pattern: "*.{phyi}"
  - phys:
      type: file
      description: Multiple sequence alignment produced in PHYLIP sequential format
      pattern: "*.{phys}"
  - html:
      type: file
      description: Multiple sequence alignment produced in HTML format
      pattern: "*.{html}"
  - tree:
      type: file
      description: NJ or UPGMA tree in Newick format produced from a multiple sequence alignment
      pattern: "*.{tree}"
  - log:
      type: file
      description: Log file of MUSCLE run
      pattern: "*{.log}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@MGordon"