Consider updating the doublet module to run on filtered files

[sjspielman]

We previously implemented the doublet detection module to run on processed files. However, this might not have been ideal since the method recommends to run on objects that have not been filtered beyond removing empty droplets. We therefore might consider updating that module to run on filtered instead.

That said we're also adding doublet detection into scpca-nf which is where we will encourage people to find this information in this future, so this workflow update may not be crucial.