name: bismark_report
description: Collects bismark alignment reports
keywords:
    - bismark
    - qc
    - methylation
    - 5mC
    - methylseq
    - bisulphite
    - 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"