name: "gunc_mergecheckm"
description: Merging of CheckM and GUNC results in one summary table
keywords:
  - gunc
  - checkm
  - summary
  - 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 ]
  - gunc_file:
      type: file
      description: Path of a gunc_scores.tsv file (mandatory)
      pattern: "*.{bam,cram,sam}"
  - checkm_file:
      type: file
      description: Output TSV from CheckM qa (ideally with -o 2 extended format)  (mandatory)
      pattern: "*.{bam,cram,sam}"

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"
  - tsv:
      type: file
      description: Merged checkm/gunc results in TSV format
      pattern: "*.tsv"

authors:
  - "@jfy133"
