David Laehnemann

I can confirm, that adding `-DCBC_THREAD_SAFE` to a `coinbrew` install avoids race conditions between separate instances (with separate problems) of calling the C API that run at the same time....

Well spotted and thanks for documenting this in so much detail, with good suggestions. You and anybody using this pipeline is welcome to implement this via a PR, and we...

Sure, that could be a root cause here. Or simply overlooking some details... Does your workflow above follow the GATK best practices and do you actively maintain it? It might...

Yes, the workflow downloads the reference from Ensembl based on the config file, because sadly things like the exact naming of chromosomes matters a lot for a bunch of downstream...

Hi @jonathandmoore, thanks for the feedback. Let's try to develop some more fitting and generic solution! Two quick thoughts already: 1. We use 'group' in a different context, to define...

Actually, some more thoughts from an internal discussion: `explanatory variable` has a connotation of causality, that is problematic. So maybe not the best choice. Something that speaks for `condition` is...

Thanks for so clearly identifying this problem, @neavemj. Would you like to suggest the respective needed change in a pull request, so we can document this as your contribution to...

The `3` was just to a number in there instead of some placeholder, so a different default for different tools makes sense. I think the most important point is getting...

Just pinging in some people to get some more opinions and ideas on this: @johanneskoester, @jafors, @tedil, @christopher-schroeder

I have to admit I don't fully understand the solutions you propose, but is that something that would make sense to have in [snakemake-wrapper-utils](https://github.com/snakemake/snakemake-wrapper-utils)?