Default 'flavour' behaviour for singularity preprocessing

[benjacobs123456]

Hi @zktuong thanks again for a super package. A quick question - since the update to the singularity for preprocessing I've noticed I am losing far more TRB contigs during filtering without having changed any of the flags. On inspection these contigs are being removed because a large number are lacking TRBD calls (where previously they had a call). Specifying --flavour "original" gives me sensible looking results and allows me to retain a large number of cells I would otherwise chuck, but I just wanted to check why this change has occurred now so that I can be sure there's not some funny issue with my data - was there a change to the default for the --flavour flag? Thanks so much!

Ben

[benjacobs123456]

Apologies, I have found the answer in the docs - https://sc-dandelion.readthedocs.io/en/latest/notebooks/1_dandelion_preprocessing-10x_data.html. Sorry to bother!