Gregor Sturm

Even though not as efficient, would it work to set the nextflow `scratch` directive to have Xeniumranger work outside the fusion FS?

How can I find out what's the font that is missing? 🙈

> so we would double the execution of the mtx conversions? one to at least have it before cellbender, and one again afterwards? only for filtered/unfiltered (i.e. what comes out...

Which one(s) are those specifically? only anndataR?

run ir_dist on a dask cluster: https://github.com/scverse/scirpy/pull/512#pullrequestreview-2037420362

There's also the DREAM method from the bioconductor package `variancePartition` which is an extension of limma for linear mixed effects models: https://gabrielhoffman.github.io/variancePartition/articles/dream.html It allows to specify random effects using an...

DREAM is now implemented in the `dev` branch. As this is the more general solution, I think we can close this issue.

Depends on https://github.com/MultiQC/MultiQC/pull/2861

Thanks for raising the issue, agree stderr/stdout and exit code should be forwarded. This should be fixed at the `nf-core/modules` level and likely also affects the spaceranger and cellranger multi...

No idea. But it shouldn't be hard to capture the exit code from the subprocess call and then do `sys.exit(exitcode)` in Python.