name: bbmap_bbsplit
description: Split sequencing reads by mapping them to multiple references simultaneously
keywords:
  - align
  - map
  - fastq
  - genome
  - reference
tools:
  - bbmap:
      description: BBMap is a short read aligner, as well as various other bioinformatic tools.
      homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
      documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
      tool_dev_url: None
      doi: ""
      licence: ["UC-LBL license (see package)"]

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: directory
      description: Directory to place generated index
      pattern: "*"
  - primary_ref:
      type: path
      description: Path to the primary reference
      pattern: "*"
  - other_ref_names:
      type: list
      description: List of other reference ids apart from the primary
  - other_ref_paths:
      type: list
      description: Path to other references paths corresponding to "other_ref_names"
  - only_build_index:
      type: string
      description: true = only build index; false = mapping

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - index:
      type: directory
      description: Directory with index files
      pattern: "bbsplit"
  - primary_fastq:
      type: file
      description: Output reads that map to the primary reference
      pattern: "*primary*fastq.gz"
  - all_fastq:
      type: file
      description: All reads mapping to any of the references
      pattern: "*fastq.gz"
  - stats:
      type: file
      description: Tab-delimited text file containing mapping statistics
      pattern: "*.txt"

authors:
  - "@joseespinosa"
  - "@drpatelh"
