WackerO

yeah, I've had the same issue...So far my browser can handle the report, but it does take a noticeable time to load. I'm wondering also if we could make some...

Hey there @BEFH, it would indeed be great if you could open some PRs for this! The first thing would be to change the [deseq2 module](https://github.com/nf-core/modules/tree/master/modules/nf-core/deseq2/differential). I think if possible,...

Hmm, I'm not sure if adding another param would be the best solution. As this concerns the contrasts, I think probably your other two suggestions make more sense. The check...

I'm not quite sure what you mean by Type I or II SS, but according to the [DESeq2 vignette](https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html), the order of variables in the design does not matter (search...

Hey @ctuni, yes, that sounds about right. If you find a suitable dataset in the test-datasets repo, I think you'll only need to open a PR for the contrasts file,...

Hey there, the --matrix parameter is actually not required. For the geo_soft_file study_type option, you don't need to input a matrix but rather a GEO identifier.

@Nicobouch sorry I saw your comment only now D: No, not yet, I'm currently working on another feature

Hey there, thanks for the bug report! Without the dataset, I won't be able to look into this. Maybe someone else stumbles across this error as well and can share...

Hello @tracelail, thanks for the dataset! The error is caused by the NA values in your samplesheet 🙂 I tried running the pipeline again after filling those in with a...

Hey Fernando, you should definitely be able to run the pipeline on rnaseq output, but unless you share some information about your command and the input files you used as...