name: mafft
description: Multiple sequence alignment using MAFFT
keywords:
  - msa
  - multiple sequence alignment
tools:
  - mafft:
      description: Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform
      homepage: https://mafft.cbrc.jp/alignment/software/
      documentation: https://mafft.cbrc.jp/alignment/software/manual/manual.html
      tool_dev_url: https://mafft.cbrc.jp/alignment/software/source.html
      doi: "10.1093/nar/gkf436"
      licence: ["BSD"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fasta:
      type: file
      description: FASTA file containing the sequences to align
      pattern: "*.{fa,fasta}"
  - addsequences:
      type: file
      description: FASTA file containing sequences to align to the sequences in `fasta`
      pattern: "*.{fa,fasta}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - fas:
      type: file
      description: Aligned sequences in FASTA format
      pattern: "*.{fas}"

authors:
  - "@MillironX"
