Gregor Sturm

At least for paired end data, fastp docs say there's no added value to specifying the adapters compared to autodetection: > For PE data, the adapters can be detected by...

It currently wants a comma separated string, e.g. "bclconvert,samshee" A list would be a bit more elegant when working with yaml params, but I don't know if there's a good...

We just need to agree on one canonical format that's used everywhere. One of the first steps of the pipeline should be to convert whatever input format (SummarizedExperiment, CSV, TSV,...

> start getting into hacky inter-language things (they never work that well). I used to share that sentiment, but the situation has improved lately, by, well, not using hacks (such...

One motivation would also be to make the interoperability with nf-core/rnaseq (and possibly other pipelines) simpler: > Outputs from nf-core/rnaseq and other tximport-processed results > The nf-core RNAseq workflow incorporates...

Could you elaborate on how the samplesheet would need to look like? If it's just about having additional columns, I think it would be fine. More general, we should think...

Personally I like to have all files explicitly listed in the samplesheet, also for consistency with other aligners. Possible alternative: Add an additional column `sample_type` to the samplesheet. The column...

The corresponding module has been merged: https://github.com/nf-core/modules/pull/3229

both cellranger-arc and cellranger-multi are implemented. Although cellranger-arc still needs tests (#290)

Have you also considered omnipathdb? It contains a wide range of databases including PROGENy, collecTRI, GO, CytoSig (see also #367) and can be queried using R, Python or a web...