name: biscuit_blaster

description: A fast, compact one-liner to produce duplicate-marked, sorted, and indexed BAM files 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/biscuitblaster/
      tool_dev_url: https://github.com/huishenlab/biscuit
      doi: ""
      licence: ["MIT"]
  - samblaster:
      description: |
        samblaster is a fast and flexible program for marking duplicates in read-id grouped paired-end SAM files.
        It can also optionally output discordant read pairs and/or split read mappings to separate SAM files,
        and/or unmapped/clipped reads to a separate FASTQ file.
        By default, samblaster reads SAM input from stdin and writes SAM to stdout.
      homepage: None
      documentation: https://github.com/GregoryFaust/samblaster
      tool_dev_url: https://github.com/GregoryFaust/samblaster
      doi: "10.1093/bioinformatics/btu314"
      licence: ["MIT"]
  - samtools:
      description: |
        SAMtools is a set of utilities for interacting with and post-processing
        short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
        These files are generated as output by short read aligners like BWA.
      homepage: http://www.htslib.org/
      documentation: hhttp://www.htslib.org/doc/samtools.html
      doi: 10.1093/bioinformatics/btp352
      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}"
  - bai:
      type: file
      description: Output BAM index
      pattern: "*.{bai}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@njspix"