name: eggnog_download
description: Assists in downloading eggNOG fomatted databases
keywords:
  - annotation
  - download
tools:
  - eggnog:
      description: Fast genome-wide functional annotation through orthology assignment.
      homepage: http://eggnog-mapper.embl.de/
      documentation: https://github.com/eggnogdb/eggnog-mapper/wiki
      tool_dev_url: https://github.com/eggnogdb/eggnog-mapper
      doi: "10.1093/molbev/msab293"
      licence: ['AGPL v3']

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]

output:
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - db:
      type: file
      description: the eggNOG annotation databases
      pattern: "*.db*"
  - proteins:
      type: file
      description: Diamond database of eggNOG sequences
      pattern: "*.dmnd"
  - hmmer:
      type: folder
      description: HMMER database of eggNOG sequences
      pattern: "hmmer/"
  - mmseqs:
      type: folder
      description: MMseqs2 database of eggNOG sequences
      pattern: "mmseqs/"
  - pfam:
      type: folder
      description: PFAM database of eggNOG sequences
      pattern: "pfam/"

authors:
  - "@rpetit3"
