Gregor Sturm

Closing this for now, feel free to reopen if you are still having issues.

You could also use [jupytext](https://github.com/mwouts/jupytext/) to save your jupyter notebooks as `Rmd` or plain `R` files and apply styler on them.

Thanks @ilia-kats. We thought that `hatch test --cover` already creates the coverage report, but that doesn't seem to be the case. Your solution will certainly work, I'm just wondering if...

@ilia-kats, can you confirm ``` hatch run hatch-test.py${{ matrix.python }}:coverage xml ``` works for you?

This should be fixed in dev now. Would be great if you could give it a try and let us know if there are still any issues!

@klkeys, @apeltzer for me an open discussion is whether the renaming should be a separate module or not - would appreciate additional opinions: https://github.com/nf-core/modules/pull/4802#pullrequestreview-1843492577 In the past I opted for...

> Currently, emptydrops will not be performed for cellranger/multi as I am not sure if it is relevant. https://github.com/nf-core/scrnaseq/blob/247-support-for-10x-ffpe-scrna/workflows/scrnaseq.nf#L278 I think it's still relevant, at least when it runs in...

> One question that comes up from that, is: whether should we add the ensembl references used in the nf-core/test-datasets or not. Ideally, yes, but I don't really care tbh...

I did observe the long runtime and maybe we should consider requesting more CPUs for cellranger multi. I didn't observe any excessive disk usage, at least it stayed well below...

Ok. I think I'm done with the documentation.