name: bbmap_align
description: write your description here
keywords:
  - align
  - map
  - fasta
  - 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 ]
  - fastq:
      type: file
      description: |
          List of input FastQ files of size 1 and 2 for single-end and paired-end data,
          respectively.
  - ref:
      type: file
      description: |
          Either "ref" a directory containing an index, the name of another directory
          with a "ref" subdirectory containing an index or the name of a fasta formatted
          nucleotide file containg the reference to map to.

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - version:
      type: file
      description: File containing software version
      pattern: "versions.yml"
  - bam:
      type: file
      description: BAM file
      pattern: "*.{bam}"

authors:
  - "@erikrikarddaniel"