1.0.1

Removed wording indicating pipeline can be used for exomes.

1.0.0

• Added description in Readme.
• Moved workflow block to the top of the wdl.
• Made docker variable that has a default but can be changed using gitc_docker_override variable.

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 GATK3 and related tools (BWA, Picard). It includes the core workflow WDL, a JSON of inputs for the WGS use case (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.