name: biscuit_epiread
description: |
  Summarizes read-level methylation (and optionally SNV) information from a
  Biscuit BAM file in a standard-compliant BED format.
keywords:
  - biscuit
  - DNA methylation
  - WGBS
  - scWGBS
  - bisulfite sequencing
  - aligner
  - bam
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/epiread_format/
      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 ]
  - bam:
      type: file
      description: Biscuit BAM file
  - bai:
      type: file
      description: BAM index
  - snp_bed:
      type: file
      description: BED file containing SNP information (optional)
  - index:
      type: dir
      description: Biscuit genome index directory (generated with 'biscuit index')
      pattern: "BiscuitIndex"

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

authors:
  - "@njspix"