name: gunc_run
description: Detection of Chimerism and Contamination in Prokaryotic Genomes
keywords:
  - prokaryote
  - assembly
  - genome
  - quality control
  - chimeras
tools:
  - gunc:
      description: Python package for detection of chimerism and contamination in prokaryotic genomes.
      homepage: https://grp-bork.embl-community.io/gunc/
      documentation: https://grp-bork.embl-community.io/gunc/
      tool_dev_url: https://github.com/grp-bork/gunc
      doi: "10.1186/s13059-021-02393-0"
      licence: ['GNU General Public v3 or later (GPL v3+)']

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fasta:
      type: file
      description: FASTA file containing contig (bins)
      pattern: "*.fa"
  - db:
      type: file
      description: GUNC database file
      pattern: "*.dmnd"

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"
  - maxcss_levels_tsv:
      type: file
      description: Output file with scores for a taxonomic level with the highest CSS score
      pattern: "*.tsv"
  - all_levels_tsv:
      type: file
      description: Optional output file with results for each taxonomic level
      pattern: "*.tsv"

authors:
  - "@jfy133"