name: bbmap_index
description: This module calls bbmap.sh to create an index from a fasta file, ready to be used by bbmap.sh in mapping mode.
keywords:
  - mapping
  - index
  - fasta
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 optional parameters to bbmap.sh
        e.g. [ id:'test', single_end:false ]
  - fasta:
      type: fasta
      description: fasta formatted file with nucleotide sequences
      pattern: "*.{fna,fa,fasta}"

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: "*.{version.txt}"
  - db:
      type: directory
      description: Directory with index files
      pattern: "ref"

authors:
  - "@daniellundin"