name: biscuit_bsconv
description: Summarize and/or filter reads based on bisulfite conversion rate
keywords:
  - biscuit
  - DNA methylation
  - WGBS
  - scWGBS
  - bisulfite sequencing
  - aligner
  - bam
  - filter

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/subcommand_help.html#biscuit-bsconv
      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: BAM file contained mapped reads
  - bai:
      type: file
      description: BAM file index
  - 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 ]
  - bsconv_bam:
      type: file
      description: Output BAM file containing filtered read alignments
      pattern: "*.{bam}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@njspix"