name: checkm_qa
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
  - qa
  - quality assurnce
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 ]
  - analysis_dir:
      type: file
      description: Directory containing output of checkm/analyze or checkm/lineage_wf etc.
      pattern: "*"
  - marker_file:
      type: file
      description: Marker file specified during checkm/analyze or produced by checkm/{lineage,taxonomy}_wf
      pattern: "*.ms"
  - coverage_file:
      type: file
      description: File containing coverage of each sequence (generated by checkm coverage)
  - exclude_marker_file:
      type: file
      description: File specifying markers to exclude from marker sets

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"
  - output:
      type: file
      description: "Default completeness statistics in various formats, as specified with --out_format (excluding option: 9)"
      pattern: "*.txt"
  - fasta:
      type: file
      description: Output in fasta format (only if --out_format 9)
      pattern: "*.fasta"

authors:
  - "@jfy133"