Lukas Heumos

Suggested by @ivirshup -> Just use intersphinx in the notebook. Can add more extensions _via_ https://jupyterbook.org/en/stable/advanced/sphinx.html Will need to play around with things.

We'll need to go through the book to harmonize the style: - [ ] Same style for "key takeaways" - [ ] Add traffic lights to all chapters - [...

Integration chapter improvements

9

Taken from @lazappi great list of TODOs in his PR with some additions of mine: Todo: - [ ] Decide on the "batch correction"/"data integration" terminology - [ ] Update...

Enable Binder

1

Host own Binder service https://binderhub.readthedocs.io/en/latest/ and then point Jupyter Book to that BinderHub's URL

https://github.com/pezmc/biblatex-check

**Advanced: Interactive visualization** - [ ] host our preprocessed example dataset on the [cellxgene data portal](https://cellxgene.cziscience.com/) - [ ] add chan zuckerberg lab to the acknowledgements in paper - [...

Missing conda recipes

2

- [x] cellhashr - [x] gmmdemux - [ ] Souporcell - [x] Vireo - [x] cellsnp (just cellsnp lite in recipes) - [x] freemuxlet - [x] scsplit

- [ ] https://github.com/nf-core/modules/issues/5064 - [ ] https://github.com/nf-core/modules/issues/5065 - [ ] https://github.com/nf-core/modules/issues/5066 - [ ] https://github.com/nf-core/modules/issues/5067 - [ ] https://github.com/nf-core/modules/issues/5068 - [ ] https://github.com/nf-core/modules/issues/5069 - [ ] https://github.com/nf-core/modules/issues/5070 - [...

- [x] Create a new nf-core branch - [x] Recreate the the pipeline starting with the template - [x] Add missing conda recipes #46 - [x] Add modules for the...

``` - name: Run pipeline with test data run: | nextflow run ${GITHUB_WORKSPACE} -profile test,conda --souporcell False --generate_anndata False ``` Currently we're only testing souporcell. Ideally, we should test all...