name: checkm_lineagewf
description: CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.
keywords:
  - checkm
  - mag
  - metagenome
  - quality
  - isolates
  - microbes
  - single cells
  - completeness
  - contamination
  - bins
  - genome bins
tools:
  - checkm:
      description: Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
      homepage: https://ecogenomics.github.io/CheckM/
      documentation: https://github.com/Ecogenomics/CheckM/wiki
      tool_dev_url: https://github.com/Ecogenomics/CheckM
      doi: "10.1101/gr.186072.114"
      licence: ["GPL v3"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fasta:
      type: file
      description: One or a list of multiple FASTA files of each bin, with extension defined with the fasta_ext value
      pattern: "*.{$fasta_ext}"
  - fasta_ext:
      type: value
      description: The file-type extension suffix of the input FASTA files (e.g., fasta, fna, fa, fas)
  - db:
      type: directory
      description: Optional directory pointing to checkM database to prevent re-downloading

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'sample', bin:'1' ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - checkm_output:
      type: directory
      description: CheckM output directory
      pattern: "*/"
  - checkm_output:
      type: file
      description: Lineage markfer file
      pattern: "lineage.ms"
  - checkm_tsv:
      type: file
      description: CheckM summary completeness statistics table
      pattern: "*.tsv"

authors:
  - "@jfy133"
