Final thing I hope: based on this commit it appears you should be able to specify whether or not to include intronic reads in cellranger count / multi using the sample sheet. However in cellranger multi this appears to be ignored:

WARN: Found the following unidentified headers in 260708_mini_nfcore_sample_sheet.csv:
        - include_introns

And the cellranger QC confirms this:

Include Introns true

(I set to false for all samples in the sample sheet) Is this expected behavior / user error, or should I open an issue?

The commit you linked seems to be only present in a user fork, not in the official pipeline from what I can see. So this probably means that your original issue still has not really been tackled

Ah, understood, thank you. The fix in that issue works very well for

cellranger count

, but not for

cellranger multi

. I will see what I can find out.