name: "eggnog_mapper"
description: Performs functional annotation using EggNOG-mapper
keywords:
  - eggnog
  - mapper
  - functional annotation
  - orthology
input:
  - meta:
      type: map
      description: Groovy Map containing sample information
  - fasta:
      type: file
      description: Input FASTA file
      pattern: "*.{fa,fasta,fna}"
  - eggnog_files:
      type: directory
      description: Directory containing EggNOG database files
      pattern: "eggnog/*"
output:
  - meta:
      type: map
      description: Groovy Map containing sample information
  - hits:
      type: file
      description: EggNOG-mapper hits file
      pattern: "*.emapper.hits.gz"
  - seed_orthologs:
      type: file
      description: EggNOG-mapper seed orthologs file
      pattern: "*.emapper.seed_orthologs.gz"
  - annotations:
      type: file
      description: EggNOG-mapper annotations file
      pattern: "*.emapper.annotations.gz"
  - emappertsv:
      type: file
      description: EggNOG-mapper TSV file
      pattern: "*.emapper.tsv.gz"
  - xlsx:
      type: file
      description: EggNOG-mapper annotations in Excel format
      pattern: "*.emapper.annotations.xlsx"
  - orthologs:
      type: file
      description: EggNOG-mapper orthologs file
      pattern: "*.emapper.orthologs.gz"
  - genepred:
      type: file
      description: EggNOG-mapper gene prediction FASTA file
      pattern: "*.emapper.genepred.fasta.gz"
  - gff:
      type: file
      description: EggNOG-mapper GFF file
      pattern: "*.emapper.gff.gz"
  - no_anno:
      type: file
      description: FASTA file of sequences without annotations
      pattern: "*.emapper.no_annotations.fasta.gz"
  - pfam:
      type: file
      description: EggNOG-mapper Pfam annotations file
      pattern: "*.emapper.pfam.gz"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@danilodileo"
