# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: "foldmason_easymsa"
description: Aligns protein structures using foldmason
keywords:
  - alignment
  - MSA
  - genomics
  - structure
tools:
  - "foldmason":
      description: "Multiple Protein Structure Alignment at Scale with FoldMason"
      homepage: "https://github.com/steineggerlab/foldmason"
      documentation: "https://github.com/steineggerlab/foldmason"
      tool_dev_url: "https://github.com/steineggerlab/foldmason"
      doi: "10.1101/2024.08.01.606130"
      licence: ["GPL v3"]
      identifier: biotools:foldmason

input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. `[ id:'sample1', single_end:false ]`
    - pdbs:
        type: file
        description: Input protein structures in PDB format.
        pattern: "*.{pdb,mmcif}"
  - - 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:
  - msa_3di:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1', single_end:false ]`
      - "${prefix}_3di.fa${compress ? '.gz' : ''}":
          type: file
          description: Fasta file containing the multiple sequence alignment with 3Di
            alphabet
          pattern: "*.{fa}"
  - msa_aa:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1', single_end:false ]`
      - "${prefix}_aa.fa${compress ? '.gz' : ''}":
          type: file
          description: Fasta file containing the multiple sequence alignment with Amino
            Acid alphabet
          pattern: "*.{fa}"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@luisas"
maintainers:
  - "@luisas"
