nextstrain
Omicron only
This PR adds an example which produces an omicron-only build. Viewable here: https://nextstrain.org/staging/ncov/omicron/2022-04-20
To do this we have to modify the rules and add an extra (optional) parameter config["files"]["include_for_subsampling"] so that we can include a set of strains for the alignment and subsequently exclude them for the tree building stage.
The resulting build has mutations in the correct co-ordinate system, but note that the ancestral state is the inferred omicron ancestral state, not the canonical Wuhan state. For instance, the root has S:501Y.
One limitation of the implementation here is that you cannot have an omicron-only build within the larger (core) Nextstrain builds because the choice of which strains to include/exclude is per-workflow, not per-build.
