2.1.1

• Updated default GATK docker to 4.2.0.0
• Updated genome-in-the-cloud docker to 2.4.7-1603303710
• Switched to docker to gcr
• Added dockerstore yml file

2.1.0

• Added more description for the workflow
• Updated default gatk docker to 4.1.8.1

2.0.0

Updated workflow to WDL1.0.
Added defaults to disk and memory parameters.

1.1.0

Updated docker to Gatk 4.1.0.0

1.0.1

• Removed wording indicating pipeline can be used for exomes.

1.0.0

• Updated Picard commands to use gatk4 instead of Picard tool in gotc docker.
• Update gatk docker to 4.0.4.0

Updated WDL name to reflect use of gatk4

To ensure we can differentiate workflows that use GATK3 vs GATK4 after they've been downloaded, we are now including the gatk major version in the wdl filename itself.

Initial release

This is the initial release of the workflow for pre-processing high-throughput sequence data from unmapped BAM (uBAM) to a clean BAM ready for variant discovery analysis using GATK4 and related tools (BWA, Picard). It includes the core workflow WDL, a JSON of inputs for the WGS use case and one for the exome use case (both against the hg38 reference), and a JSON of generic options for running via Cromwell on the Google Pipelines API (PAPI).

Requirements / caveats

The workflow uses hardcoded references to executables. It should be runnable on any platform that supports WDL. The included JSON points to data files hosted on the Google Cloud Storage platform.