Gregor Sturm

yes, users are expected to understand how this works if they use formulas and contrast strings. One thing we should consider is how to explicitly set the baseline level of...

A bioconductor release is planned, isn't it @lazappi? I think conda recipes are built for all bioconductor packages, so we'll get it "for free" then. So for now, I'd be...

anndataR is now officially part of bioconductor. @lazappi do you know why the corresponding `bioconductor-anndatar` package does not exist yet on bioconda?

Does it make sense to adjust that in https://github.com/nf-core/scrnaseq/pull/435? In the standard `h5ad` object, I think I'd prefer only gene expression to be there. If someone needs they other features,...

It would be great if you could take a look, but it's better to wait until #369 is merged because @fmalmeida already made some changes to this (but without the...

#369 is merged now. I actually think that most/all points are adressed above. @kopichris, would you be up for testing the behavior and check if there are still some pain...

> I ran the test,conda profile and received the following error in the NFCORE_SCRNASEQ:SCRNASEQ:H5AD_CONVERSION: ANNDATAR_CONVERT process: Error in library(anndataR) : there is no package called ‘anndataR’. I suspect this is...

@atrigila this also looks like an excellent issue to onboard @JeronimoVazquez

It should be totally possible to select a samplesheet schema based on a parameter (by passing a GString to [`samplesheetToList`](https://nextflow-io.github.io/nf-schema/latest/samplesheets/samplesheetToList/). Also JSON schema supports including schemas using [`allOf`](https://json-schema.org/understanding-json-schema/reference/combining). Like that...

Hi @saraterzo, thank you for working on this! I'll try to find time this week to give it a proper review.