Gregor Sturm

I would have totally expected both alevin and star to only use the number of nucleotides from R1 that is specified in the chemistry definition. In this case you run...

This should totally be supported. For me the question is if we can make alevin/starsolo directly work with the untrimmed reads (and what would be the appropriate command line options...

This would be possible using custom nextflow configuration files, see here: https://nf-co.re/docs/usage/getting_started/configuration#customising-tool-arguments It is also possible to override the used container version the same way, however there's no guarantee that...

I don't think there's anything to fix in scrnaseq for now. Either `inspect` needs to be improved, or the nf-core template.

Note that we have already implemented some of the topics from "Report" in https://github.com/nf-core/differentialabundance/pull/545 (currently a bunch of merge conflicts, will update shortly). For splitting the report, see https://github.com/nf-core/differentialabundance/pull/535

@maltekuehl, could the paralellization you implemented be pushed up to the abstract base class? Then also wilcoxon and ttest would benefit from it. In that case, would it even be...

I still need to give it a proper review, didn't have the time yet

Hi, thanks for opening the issue! I think mapping `contig_id` to `sequence_id` in both `read_10x_csv` and `read_10x_json` is the correct thing to do. This would allow you to retreive it...

@pinin4fjords, do you have thought on this? which option would you prefer?

Warnings are treated as errors. ``` /home/docs/checkouts/readthedocs.org/user_builds/scirpy/checkouts/542/docs/tutorials/tutorial_5k_bcr.ipynb:40002: WARNING: could not find bibtex key "null.2022" /home/docs/checkouts/readthedocs.org/user_builds/scirpy/checkouts/542/docs/tutorials/tutorial_5k_bcr.ipynb:40005: WARNING: could not find bibtex key "Suo.2023" /home/docs/checkouts/readthedocs.org/user_builds/scirpy/checkouts/542/docs/tutorials/tutorial_5k_bcr.ipynb:60003: WARNING: could not find bibtex key "Lefranc.2003"...