scanvi refmap fails when query_celltype not specified in yaml

[wlason]

In pipeline.yaml for refmap, specifying query_celltype is optional and will default to celltype if None, however this line doesn't take into account that query_celltype may be unspecified, so the script fails if it is not specified.

panpipes/panpipes/python_scripts/refmap_scvitools.py

Line 327 in 0cb7826

L.warn("Acc: {}".format(np.mean(full_predictions == adata_full.obs.celltype)))

If query_celltype is None, we need to create a new column in obs called celltype first, or skip this if-statement.

[bio-la]

hey @wlason,
this line refers to the concatenated reference and query datasets, after the celltype prediction using the trained scanvi model. in the documentation
we specify that the query has to contain a column with the same name as the label (celltype in this case) you need to transfer from the reference, filled with "unknown". (these are standard scvi-tools rules for scanvi, not related to panpipes)

can you tell me if you found an issue with these instructions? thank you for reporting!