name: methyldackel_extract
description: Extracts per-base methylation metrics from alignments
keywords:
  - methylation
  - 5mC
  - methylseq
  - bisulphite
  - bisulfite
  - consensus
  - bedGraph
  - bam
  - cram
tools:
  - methyldackel:
      description: |
        Methylation caller from MethylDackel, a (mostly) universal methylation extractor
        for methyl-seq experiments.
      homepage: https://github.com/dpryan79/MethylDackel
      documentation: https://github.com/dpryan79/MethylDackel/blob/master/README.md
      licence: ["MIT"]
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 ]
  - bedgraph:
      type: file
      description: bedGraph file, containing per-base methylation metrics
      pattern: "*.bedGraph"
  - methylkit:
      type: file
      description: methylKit file, containing per-base methylation metrics
      pattern: "*.methylKit"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@phue"
