Johannes Köster

This looks very good! Besides some very minor things, it is exactly like a perfect snakemake workflow should be. Do you intend to move this over here? 1. At least...

By default, the wrapper uses a hardcoded conda environment (see [here](https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/bwa/mem.html#software-dependencies)). By this, we ensure stability. If this shall be overridden, the user can specify a custom conda environment within...

@jrderuiter is your workflow ready for moving here? It does not need to be perfect, we can mark it as WIP.

Hey @johne and @SilasK sorry for being so late about this. I completely missed the notifications. Very nice pipelines! Both of them could be included here relatively quickly I think....

The error comes from using a newer version of the star wrapper. The pipeline is designed to use version 0.19.4 of the wrapper. Did you change that version in any...

That bug was present in a previous version of Snakemake, but it should be fixed with the latest version of Snakemake and the pipeline. Can you confirm?

Better :-). Now, I suggest having a look at the log file of the failed rule: `logs/star/B-1.log`.

I think the true solution is to just require people to specify a design matrix (via a formula over column names) instead of naming one column in a predefined way....

Yes, reversing is right.

For testing the workflows here, we use travis ci so far.