cellranger-analysis module: potential issue with dual genome reference

[AntoniaChroni]

What analysis module should be updated and why?

There might be an issue with the cellranger-analysis module when using dual genome reference.

From our discussion with @sharonfreshour:

• The dual reference runs CellRanger's metrics include some that are specific to either the human or the mouse genomes used and those are labeled by CellRanger based on the reference name. For example, when the summarize-cellranger-results.py script is looking for a column named mm10 ..., it should be looking for a column named GRCm39 ... based on how CellRanger itself will name the metrics columns for the new GRCm39 reference.

What changes need to be made? Please provide enough detail for another participant to make the update.

We will not make any changes for the moment.

[AntoniaChroni]

@CodyRamirez What are your thoughts on this?

[sharonfreshour]

Should we consider doing an additional test run of the module using the dual reference (similar to how we plan to do a test run with the human reference)?