name: biscuit_qc
description: Perform basic quality control on a BAM file generated with Biscuit
keywords:
  - biscuit
  - DNA methylation
  - WGBS
  - scWGBS
  - bisulfite sequencing
  - index
  - BAM
  - quality control

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-qc
      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 produced using Biscuit

output:
  - biscuit_qc_reports:
      type: file
      description: |
        Summary files containing the following information:
          - CpG retention by position in read
          - CpH retention by position in read
          - Read duplication statistics
          - Insert size distribution
          - Distribution of mapping qualities
          - Proportion of reads mapping to each strand
          - Read-averaged cytosine conversion rate for CpA, CpC, CpG, and CpT
      pattern: "*.txt"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@njspix"