name: "eukulele_search"
description: Performs taxonomic classification using EUKulele
keywords:
  - eukulele
  - taxonomy
  - classification
  - eukaryotes
input:
  - meta:
      type: map
      description: Groovy Map containing sample information
  - fasta:
      type: file
      description: Input protein FASTA file
      pattern: "*.{faa,fasta}"
  - dbname:
      type: value
      description: Name of the database to use for classification
  - eukdb:
      type: directory
      description: Directory containing EUKulele reference database
output:
  - meta:
      type: map
      description: Groovy Map containing sample information
  - taxonomy_estimation:
      type: file
      description: EUKulele taxonomy estimation output
      pattern: "*/taxonomy_estimation/*.out.gz"
  - taxonomy_counts:
      type: file
      description: EUKulele taxonomy counts output
      pattern: "*/taxonomy_counts/*.csv.gz"
  - diamond:
      type: directory
      description: DIAMOND alignment results
      pattern: "*/mets_full/diamond/*"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@danilodileo"
