Nico Trummer

> Besides that, is the pipeline going to download the entire reference genome (assuming only genome is set), even though no module uses the fasta (e.g., souporcell is not set...

Depending on what exactly you want to test, you could also override the `genomes` parameter in your run. You could add the following to a `nextflow.config` file in your launchdir...

Hey, the problem was that tfactivity expected `gene` feature rows to be present in the GTF file. This is not the case for this, and some/many other igenomes. I know...

Should switch this to an R implementation. [This Vignette](https://cellgeni.github.io/notebooks/html/new-10kPBMC-SoupX.html) can serve as a template. Should use AnndataR if the file ends with `.h5ad` otherwise `readRDS`.

Errors might be related to [this issue](https://github.com/wheaton5/souporcell/issues/243), but need further investigation