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
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}"
    - version:
        type: file
        description: File containing software version
        pattern: "versions.yml"
authors:
    - "@phue"