name: methyldackel_mbias
description: Generates methylation bias plots from alignments
keywords:
    - methylation
    - 5mC
    - methylseq
    - bisulphite
    - methylation bias
    - mbias
    - qc
    - bam
    - cram
tools:
    - methyldackel:
        description: |
            A (mostly) universal methylation extractor
            for BS-seq experiments.
        homepage: https://github.com/brentp/bwa-meth
        documentation: https://github.com/brentp/bwa-meth
        arxiv: arXiv:1401.1129
input:
    - meta:
        type: map
        description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
    - fasta:
        type: file
        description: Input genome fasta file
        pattern: "*.{fasta,fa}"
    - fai:
        type: file
        description: FASTA index file
        pattern: "*.{fai}"
    - bam:
        type: file
        description: BAM/CRAM file
        pattern: "*.{bam,cram}"
    - bai:
        type: file
        description: BAM/CRAM index file
        pattern: "*.{bai,crai}"
output:
    - meta:
        type: map
        description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
    - txt:
        type: file
        description: Text file containing methylation bias
        pattern: "*.{txt}"
    - version:
        type: file
        description: File containing software version
        pattern: "*.{version.txt}"
authors:
    - "@phue"