name: mafft_align
description: Multiple sequence alignment using MAFFT
keywords:
  - fasta
  - 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"]
      identifier: biotools:MAFFT
  - "pigz":
      description: "Parallel implementation of the gzip algorithm."
      homepage: "https://zlib.net/pigz/"
      documentation: "https://zlib.net/pigz/pigz.pdf"
      identifier: biotools:MAFFT
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. May be gzipped or
          uncompressed.
        pattern: "*.{fa,fasta}{.gz,}"
        ontologies:
          - edam: http://edamontology.org/format_1919 # SEQUENCE-LIKE
          - edam: http://edamontology.org/format_1929 # FASTA
  - - meta2:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - add:
        type: file
        description: FASTA file containing sequences to align to the sequences in `fasta`
          using `--add`. May be gzipped or uncompressed.
        pattern: "*.{fa,fasta}{.gz,}"
        ontologies:
          - edam: http://edamontology.org/format_1919 # SEQUENCE-LIKE
          - edam: http://edamontology.org/format_1929 # FASTA
  - - meta3:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - addfragments:
        type: file
        description: FASTA file containing sequences to align to the sequences in `fasta`
          using `--addfragments`. May be gzipped or uncompressed.
        pattern: "*.{fa,fasta}{.gz,}"
        ontologies:
          - edam: http://edamontology.org/format_1919 # SEQUENCE-LIKE
          - edam: http://edamontology.org/format_1929 # FASTA
  - - meta4:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - addfull:
        type: file
        description: FASTA file containing sequences to align to the sequences in `fasta`
          using `--addfull`. May be gzipped or uncompressed.
        pattern: "*.{fa,fasta}{.gz,}"
        ontologies:
          - edam: http://edamontology.org/format_1919 # SEQUENCE-LIKE
          - edam: http://edamontology.org/format_1929 # FASTA
  - - meta5:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - addprofile:
        type: file
        description: FASTA file containing sequences to align to the sequences in `fasta`
          using `--addprofile`. May be gzipped or uncompressed.
        pattern: "*.{fa,fasta}{.gz,}"
        ontologies:
          - edam: http://edamontology.org/format_1919 # SEQUENCE-LIKE
          - edam: http://edamontology.org/format_1929 # FASTA
  - - meta6:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - addlong:
        type: file
        description: FASTA file containing sequences to align to the sequences in `fasta`
          using `--addlong`. May be gzipped or uncompressed.
        pattern: "*.{fa,fasta}{.gz,}"
        ontologies:
          - edam: http://edamontology.org/format_1919 # SEQUENCE-LIKE
          - edam: http://edamontology.org/format_1929 # FASTA
  - 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:
  fas:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.fas{.gz,}":
          type: file
          description: Aligned sequences in FASTA format. May be gzipped or uncompressed.
          pattern: "*.fas{.gz,}"
          ontologies:
            - edam: http://edamontology.org/format_2554 # ALIGNMENT FORMAT TXT
            - edam: http://edamontology.org/format_1921 # ALIGNMENT FORMAT
            - edam: http://edamontology.org/format_1984 # FASTA-ALN
  versions:
    - versions.yml:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
        ontologies:
          - edam: http://edamontology.org/format_3750 # YAML
authors:
  - "@MillironX"
maintainers:
  - "@MillironX"
  - "@Joon-Klaps"
