name: eggnog_mapper
description: Genome annotation using orthologous groups and phylogenies
keywords:
  - annotation
  - fasta
  - prokaryote
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 ]
  - fasta:
      type: file
      description: FASTA assembly file
      pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}"
  - db:
      type: folder
      description: directory containing eggNOG databases
      pattern: "*"

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"
  - hits:
      type: file
      description: Results from the search phase, from HMMER, Diamond or MMseqs2
      pattern: "*.emapper.hits"
  - seed_orthologs:
      type: file
      description: Results from parsing the hits
      pattern: "*.emapper.seed_orthologs"
  - annotations:
      type: file
      description: Results from the annotation phase
      pattern: "*.emapper.annotations"
  - xlsx:
      type: file
      description: Annotations in .xlsx format
      pattern: "*.emapper.annotations.xlsx"
  - orthologs:
      type: file
      description: List of orthologs found for each query
      pattern: "*.emapper.orthologs"
  - genepred:
      type: file
      description: Sequences of predicted CDS
      pattern: "*.emapper.genepred.fasta"
  - gff:
      type: file
      description: GFF of predicted CDS
      pattern: "*.emapper.gff"
  - no_anno:
      type: file
      description: Sequences without annotation
      pattern: "*.emapper.no_annotations.fasta"
  - pfam:
      type: file
      description: Positions of the PFAM domains identified
      pattern: "*.emapper.pfam"

authors:
  - "@rpetit3"
