Cell Ranger 'Multiplexing Capture' feature type not recognised.

[jpintar]

When I supply Cell Ranger’s Multiplexing Capture to --exclude-feature-types, the following warning is issued:

Specified 'Multiplexing Capture' using --exclude-feature-types, but this is not a valid CellRanger 
feature designation: ['Gene Expression', 'Antibody Capture', 'CRISPR Guide Capture', 'Custom', 
'Peaks']. Ensure that this feature appears in your dataset, and ensure that this log file makes note 
of the exclusion of the appropriate features below.

The log then erroneously notes:

cellbender:remove-background: Features in dataset: 33538 Gene Expression, 3 Multiplexing Capture
cellbender:remove-background: Excluding Multiplexing Capture features (output will equal input).
cellbender:remove-background:     - This results in the exclusion of 3 features.

I say ”erroneously”, because the features are in fact modified in the output.

I'm not sure about the inconsistent messages in the log, but I did make a PR (#339) to include Multiplexing Capture and a few others in the list of recognised feature types.

[sjfleming]

Thank you for the PR @jpintar , that looks like just the right fix.

I agree: the log is problematic, and what's happening is that cellbender didn't know Multiplexing Capture was an allowed feature.