Add option to not prepare __REF_DATA table to Prepare [VS-697]

[rsasch]

Since we might need to run the GvsPrepareRangesCallset.wdl in the future just to help to get the callset stats, add an optional input to not create the __REF_DATA and __SAMPLES tables, since those won't be needed.

Test runs:

• with skip_ref_ranges_tables set to true:
• with skip_ref_ranges_tables set to false
• with skip_ref_ranges_tables not set (default is false)
• GvsCallsetStatistics run
  ... after changes ...
• with only_output_vet_tables set to true
• with only_output_vet_tables set to false
• GvsCreateCohortFromSampleNames run (failed because of other issue)

[codecov]

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Additional details and impacted files

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[mcovarr]

yay! 👍

[koncheto-broad]

LGTM

[gbggrant]

Looks good. I would note that GvsCallsetStatistics no longer needs the __SAMPLE table created here. So, it too could be made optional (although it's not that expensive to make it).

[gbggrant]

Looks good! Thanks for the thorough testing.