I see you have two comments regarding the multiplet rate - one suggesting an explicit command line variable for it, else use default. And then another suggesting the command line var is not necessary at all, just default is fine - which do you prefer?

The difference between adding it as (1) a pipeline parameter (what you probably meant by 'command line variable') and (2) using a samplesheet column is that (2) allows you to specify different doublet rates per dataset. This is relevant if you mix datasets from different sequencing technologies (10X, BD Rhapsody, etc) and want specific doublet rates for each of them. If you do it like (1), then you can only set one rate for all datasets.

Samplesheet columns are defined here