Integration & annotation: consider moving cell-level annotation before integration

[mgeaghan]

Cell-level annotation doesn't need to come after integration. Additionally, the workflow could benefit from annotating cells, then assigning cell types to clusters, integrating, and then checking how well the pre-integration annotated clusters align with each other post-integration.

The new workflow would be something like:

1. QC + doublet detection + clustering
2. Annotation
3. Integration
4. Re-clustering
5. Check alignment of pre-integration and post-integration clusters
6. Re-assign cell types to post-integration clusters
7. Pseudo + DE + FEA