name: gatk4_genomicsdbimport
description: merge GVCFs from multiple samples. For use in joint genotyping or somatic
  panel of normal creation.
keywords:
  - gatk4
  - genomicsdb
  - genomicsdbimport
  - jointgenotyping
  - panelofnormalscreation
tools:
  - gatk4:
      description: |
        Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
        with a primary focus on variant discovery and genotyping. Its powerful processing engine
        and high-performance computing features make it capable of taking on projects of any size.
      homepage: https://gatk.broadinstitute.org/hc/en-us
      documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
      doi: 10.1158/1538-7445.AM2017-3590
      identifier: ""
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test']
    - vcf:
        type: list
        description: either a list of vcf files to be used to create or update a genomicsdb,
          or a file that contains a map to vcf files to be used.
        pattern: "*.vcf.gz"
    - tbi:
        type: list
        description: list of tbi files that match with the input vcf files
        pattern: "*.vcf.gz_tbi"
    - interval_file:
        type: file
        description: file containing the intervals to be used when creating the genomicsdb
        pattern: "*.interval_list"
    - interval_value:
        type: string
        description: if an intervals file has not been spcified, the value enetered
          here will be used as an interval via the "-L" argument
        pattern: "example: chr1:1000-10000"
    - wspace:
        type: file
        description: path to an existing genomicsdb to be used in update db mode or
          get intervals mode. This WILL NOT specify name of a new genomicsdb in create
          db mode.
        pattern: "/path/to/existing/gendb"
  - - run_intlist:
        type: boolean
        description: Specify whether to run get interval list mode, this option cannot
          be specified at the same time as run_updatewspace.
        pattern: "true/false"
  - - run_updatewspace:
        type: boolean
        description: Specify whether to run update genomicsdb mode, this option takes
          priority over run_intlist.
        pattern: "true/false"
  - - input_map:
        type: boolean
        description: Specify whether the vcf input is providing a list of vcf file(s)
          or a single file containing a map of paths to vcf files to be used to create
          or update a genomicsdb.
        pattern: "*.sample_map"
output:
  - genomicsdb:
      - meta:
          type: directory
          description: Directory containing the files that compose the genomicsdb workspace,
            this is only output for create mode, as update changes an existing db
          pattern: "*/$prefix"
      - $prefix:
          type: directory
          description: Directory containing the files that compose the genomicsdb workspace,
            this is only output for create mode, as update changes an existing db
          pattern: "*/$prefix"
  - updatedb:
      - meta:
          type: directory
          description: Directory containing the files that compose the updated genomicsdb
            workspace, this is only output for update mode, and should be the same path
            as the input wspace.
          pattern: "same/path/as/wspace"
      - $updated_db:
          type: directory
          description: Directory containing the files that compose the updated genomicsdb
            workspace, this is only output for update mode, and should be the same path
            as the input wspace.
          pattern: "same/path/as/wspace"
  - intervallist:
      - meta:
          type: file
          description: File containing the intervals used to generate the genomicsdb,
            only created by get intervals mode.
          pattern: "*.interval_list"
      - "*.interval_list":
          type: file
          description: File containing the intervals used to generate the genomicsdb,
            only created by get intervals mode.
          pattern: "*.interval_list"
      - list:
          type: file
          description: File containing the intervals used to generate the genomicsdb,
            only created by get intervals mode.
          pattern: "*.interval_list"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@GCJMackenzie"
maintainers:
  - "@GCJMackenzie"
