cell type annotation

[simroka]

Description of feature

Would it be possible to match cellranger annotate (see here)?

I am aware that nf-core/scdownstream is under development and will include cell type annotation. But since they serve different purposes, including this step in both pipelines might be justified.

I'm sure the topic has been thoroughly discussed in the past, I couldn't find a record of it though.

[nictru]

It is perfectly fine to have certain parts of the pipelines overlapping between scrnaseq and scdownstream. So far we discussed this mainly for QC modules (e.g. doublet detection, empty droplet detection), but I think cell type annotation should also be fine. The goal for shared modules is to add them to nf-core/modules and then pull them into the pipelines from there. But you can also contribute to one of the pipeline repos first and add it to nf-core/modules later

[simroka]

thanks for the response. I agree about the modules, didn't know the specifics though.
I saw this nf-core/scdownstream#257 just now and will check it out.

one question though - cellranger annotate requires 10x Genomics Cloud CLI Access Token.
in addition, there are limited numbers of requests per month I believe. only US/Canada can buy more.
would this rule out cellranger annotate from the start? due to the limitations, it would make sense only for the aggregated object though. cellranger aggr would be something we'd like to add too though #526