Synchronize indexes with vg autoindex, or provide an indexing WDL

[adamnovak]

Right now, the Giraffe/DV workflows want an XG, a GBWT, and a GBWTGraph .gg file, along with the minimizer and distance indexes:

vg_wdl/workflows/giraffe_and_deepvariant.wdl

Lines 23 to 25 in 1e77116

	File XG_FILE # Path to .xg index file
	File GBWT_FILE # Path to .gbwt index file
	File GGBWT_FILE # Path to .gg index file

But vg autoindex -w giraffe only wants to make a GBZ file, minimizer index, and distance index.

We should change the workflows to be able to use a GBZ in place of the .gbwt/.gg pair, and we should also enable the GBZ to be usable as a replacement for the XG.

If we want to retain compatibility with the existing sets of files, we might need to work hard on how to make it clear that some combinations of the resulting optional input arguments are allowed and others are not. Maybe we'd want different top-level WDL files consuming different sets of inputs?