name: gatk4_genomicsdbimport description: merge GVCFs from multiple samples. For use in joint genotyping or somatic panel of normal creation. keywords: - gatk4 - genomicsdbimport - genomicsdb - panelofnormalscreation - jointgenotyping 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 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" - wspace: type: path 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" - intervalfile: type: file description: file containing the intervals to be used when creating the genomicsdb pattern: "*.interval_list" - intervalval: 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" - 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: 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: 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: type: file description: File containing the intervals used to generate the genomicsdb, only created by get intervals mode. pattern: "*.interval_list" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@GCJMackenzie"