Carl Mathias Kobel

This error massage: https://github.com/snakemake/snakemake/pull/2859 might be an argument to raise the priority of this issue. Though, all the code fix does is to hide the message, so it is only...

Should be integrated in the conda test. Right now it is just "asscom2 --dry-run" because I had some weird lock? problems on the azure server.

As I have now experienced, downloads of some databases and also installation of some conda environments is unstable over time, so this really needs to be highly prioritized.

Maybe setting this up on thylakoid through cron is a good option. - [ ] todo

I have made a separate repository for this. Can't decide if it should be part of the ac2 repository, feels like it might become a bit bloated. https://github.com/cmkobel/ac2-test-battery

It is going well with this but still haven't set up a cron job on Johans.

To do, run each rule in sequence to check when the hidden dirs are created, and find a way for the rules to purge them.

Thanks! Great idea! MCFs are definitely easier to interpret than p-values for GSEA. That R package looks neat, but the KO calls are already made in the kegg_diamond rule so...

This will be solved by adding [gapseq](https://github.com/jotech/gapseq/) which calculates pathway completion fractions. It is well maintained and very powerful. Currently waiting for r-chnosz to be published on conda-forge so we...

### Genome Compass A compass for genomes. Makes you find your way. It is for genomes, it is a compass. You can _com_-pare, _ass_-emblies of _com_-munities, _com_-putationally.  Billedet...