name: biscuit_vcf2bed
description: |
  Summarizes methylation or SNV information from a Biscuit VCF in a
  standard-compliant BED file.
keywords:
  - biscuit
  - DNA methylation
  - WGBS
  - scWGBS
  - bisulfite sequencing
  - aligner
  - vcf
tools:
  - biscuit:
      description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
      homepage: https://huishenlab.github.io/biscuit/
      documentation: https://huishenlab.github.io/biscuit/docs/methylextraction.html
      tool_dev_url: https://github.com/huishenlab/biscuit
      doi: ""
      licence: ["MIT"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - vcf:
      type: file
      description: Biscuit vcf file (output of biscuit pileup)

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bed:
      type: file
      description: Gzipped BED file with methylation or SNV information
      pattern: "*.{bed.gz}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@njspix"