name: bbmap_align
description: Align short or PacBio reads to a reference genome using BBMap
keywords:
  - align
  - map
  - fasta
  - 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/software-tools/bbtools/bb-tools-user-guide/
      documentation: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/
      licence: ["UC-LBL license (see package)"]
      identifier: biotools:bbmap
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.
        ontologies: []
  - 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 containing the reference to map to.
      ontologies: []
output:
  bam:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.bam":
          type: file
          description: BAM file
          pattern: "*.{bam}"
          ontologies: []
  log:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.log":
          type: file
          description: Log file
          pattern: "*.{log}"
          ontologies: []
  versions:
    - versions.yml:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
        ontologies:
          - edam: http://edamontology.org/format_3750 # YAML
authors:
  - "@erikrikarddaniel"
maintainers:
  - "@erikrikarddaniel"
