name: bismark_report
description: Collects bismark alignment reports
keywords:
  - bismark
  - qc
  - methylation
  - 5mC
  - methylseq
  - bisulphite
  - bisulfite
  - report
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 ]
  - align_report:
      type: file
      description: Bismark alignment reports
      pattern: "*{report.txt}"
  - splitting_report:
      type: file
      description: Bismark splitting reports
      pattern: "*{splitting_report.txt}"
  - dedup_report:
      type: file
      description: Bismark deduplication reports
      pattern: "*.{deduplication_report.txt}"
  - mbias:
      type: file
      description: Text file containing methylation bias information
      pattern: "*.{txt}"
  - fasta:
      type: file
      description: Input genome fasta file
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - report:
      type: file
      description: Bismark reports
      pattern: "*.{html,txt}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@phue"
