nf-core

I think it would be good to have a module for gatk4

In some metagenomic contexts, there can be closely related species in a sample that can make read mapping to a single reference genome difficult (e.g. cross-mapping of reads between species). In this situation, it can be useful to employ competitive mapping, whereby reference genomes from closely related species are concatenated (in a multifasta), and the reads mapped to this reference. This can a

Ahoy pirates,

sister issue for theislab/sfaira#392
We would suggest to add a process to output an AnnData object. This would allow us to add new fields to Sfaira dataloaders to indicate how the raw data was processed. Detailed discussion and context in the issue above.

CC @grst @davidsebfischer

We could also overwrite the experimental design generated from the SDRF but I don't know if that gets even more confusing.
Maybe in the long run we even deprecated the "--expdesign" parameter and require an SDRF? But the "--input foo.mzML --expdesign des.tsv" is just very convenient for quick analyses.