name: bismark_methylationextractor
description: Extracts methylation information for individual cytosines from alignments.
keywords:
  - bismark
  - consensus
  - map
  - methylation
  - 5mC
  - methylseq
  - bisulphite
  - 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 ]
  - bam:
      type: file
      description: BAM file containing read alignments
      pattern: "*.{bam}"
  - 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 ]
  - bedgraph:
      type: file
      description: Bismark output file containing coverage and methylation metrics
      pattern: "*.{bedGraph.gz}"
  - methylation_calls:
      type: file
      description: Bismark output file containing strand-specific methylation calls
      pattern: "*.{txt.gz}"
  - coverage:
      type: file
      description: Bismark output file containing coverage metrics
      pattern: "*.{cov.gz}"
  - report:
      type: file
      description: Bismark splitting reports
      pattern: "*_{splitting_report.txt}"
  - mbias:
      type: file
      description: Text file containing methylation bias information
      pattern: "*.{M-bias.txt}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@phue"