name: "bismark_coverage2cytosine"
description: Relates methylation calls back to genomic cytosine contexts.
keywords:
  - bismark
  - consensus
  - map
  - methylation
  - 5mC
  - methylseq
  - bisulphite
  - bisulfite
  - bam
  - bedGraph
tools:
  - bismark:
      description: |
        Bismark is a tool to map bisulfite treated sequencing reads
        and perform methylation calling in a quick and easy-to-use fashion.
      homepage: https://github.com/FelixKrueger/Bismark
      documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
      doi: 10.1093/bioinformatics/btr167
      licence: ["GPL-3.0-or-later"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - coverage_file:
      type: file
      description: |
        A file containing methylation calls per position, in the format produced by bismark_methylation_extractor.
  - index:
      type: dir
      description: Bismark genome index directory
      pattern: "BismarkIndex"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - coverage:
      type: file
      description: A file containing methylation calls per position.
      pattern: "*.cov.gz"
  - report:
      type: file
      description: Genomic cytosine context results.
      pattern: "*report.txt.gz"
  - summary:
      type: file
      description: Cyotosine context summary report.
      pattern: "*cytosine_context_summary.txt"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@ewels"
