name: biscuit_align
description: Aligns single- or paired-end reads from bisulfite-converted libraries to a reference genome using Biscuit.
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/docs/alignment
      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 ]
  - reads:
      type: file
      description: |
        List of input fastq files of size 1 and 2 for single-end and paired-end data,
        respectively.
  - 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 ]
  - bam:
      type: file
      description: Output BAM file containing read alignments
      pattern: "*.{bam}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@njspix"