googlegenomics / gcp-variant-transforms / 1532

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Scalable vep annotation in VT (#433)

This PR improves the current annotation pipeline by:
- Add option '--shard_input_files' to shard the input files before annotations.
- Add option '--run_with_garbage_collection' to clean up the VMs in case of failure or cancellation.
- Distribute the annotation workload to VMs more evenly based on the number of variants rather than the number of files.
- Add Integration tests and published a new VEP image.

TODO: update the doc.
Tested: unit tests  & integration tests

324 of 324 new or added lines in 11 files covered. (100.0%)

6943 of 7820 relevant lines covered (88.79%)

0.89 hits per line