Gregor Sturm

AFAIK Dorothea is now obsolete in favor of [collecTRI](https://github.com/saezlab/CollecTRI). It does the same thing, it's just a more comprehensive database. It's also possible to run it through decoupleR.

It's not very well documented in scirpy, but it should be possible to define a substitution matrix in a file as supported by parasail: https://github.com/jeffdaily/parasail-python?tab=readme-ov-file#substitution-matrices and then use ```python ir.pp.ir_dist(adata,...

Did it work out?

I'll fix the tests in #4901, then they should hopefully pass here as well.

ok, that didn't work. #4901 only fixed tests for `cellranger/count`, not the other modules. And even here it now complains that it can't find the docker image.

Here we go! This (https://github.com/nf-core/modules/pull/5016/commits/9708c26fa1fc52550a7d83965d3c358442ee3df4) did the trick. Apparently `mkref` has been changed from a simple script to a Martian pipeline between 7.x and 8.x -- therefore we now need...

Hi @DongzeHE, we are of course happy to support the latest version of simpleaf and would appreciate a PR. As usual, it would be great to first update the module...

sounds good. I think we should only expose the most frequently used options on the pipeline level (and those that require an additional input file). Users can still set arbitrary...

Hi @DongzeHE, I was wondering if there are any updates on this? I'd hope that updating Simpleaf will solve issues like #253.

>> Make sure your code lints (nf-core lint). > > Sorry, I don't know what this means. The [nf-core CLI](https://github.com/nf-core/tools) provides some linting check that ensures certain quality and consistency...