[bat_int] cell cycle genes not in adata for cellxgene_census dataset

[KaiWaldrant]

Describe the bug The Metric cell_cycle_conservation fails with datasets from the Cell x Gene Census:

ValueError: cell cycle genes not in adata
 organism: human
 varnames: ['ENSG00000105792', 'ENSG00000128253', 'ENSG00000015413', 'ENSG00000164402', 'ENSG00000246375', 'ENSG00000176402', 'ENSG00000022976', 'ENSG00000123191', 'ENSG00000198283', 'ENSG00000092020']

To Reproduce https://tower.nf/orgs/openproblems-bio/workspaces/openproblems-bio/watch/ma2LsRoQarR8Z

Expected behavior A clear and concise description of what you expected to happen.

Additional context Add any other context about the problem here.

[mumichae]

Hi, so this issue comes from the fact that the cell cycle genes used are available as gene names, not Ensembl IDs. However CxG uses Ensembl IDs in the var names. I would suggest to overwrite the var_names with adata.var["feature_name"], if that column exists during the processing. Does that sound reasonable?

[rcannood]

I tend to prefer to set the var names to emsembl ids instead of the gene names, because otherwise there are duplicate var names. WDYT?

[mumichae]

In general that makes sense, but for the cell cycle metric we would still need gene symbols. Would you prefer to rename the var_names only for the metric instead?