Carl Mathias Kobel

Hi @eternal-flame-AD Thanks for considering my challenge of passing command line arguments using the config system of the Snakemake framework. It is not an easy problem to solve and I'm...

Snakemake has now been modified to allow hyphens in CLI-config strings from version 8.17.0 https://github.com/snakemake/snakemake/pull/2998 To do: CompareM2 will be updated to use this version of snakemake (or newer) asap.

Hi Rui Assuming that you want to change the path, where the databases are stored. You can set the `COMPAREM2_DATABASES` environment variable (in your conda env or in your ~/.bashrc...

Actually, many of the tables make perfectly good sense when having +1000 genomes. Maybe just check that all figures work up until 512 genomes, and then throw a warning, disclaiming...

Idea: Couldn't I just bundle the launcher into the docker image (as I do with bakta/prokka), and then somehow that environment should launch when docker runs the image.

Could be just running a dry-run on a dummy file.

Check the downloads, and that a dryrun will complete. Anything else?

Thanks for filing a bug Would you mind attaching the dbcan output (results_comparem2/samples/\/dbcan/dbcan-sub.hmm.out) and the .html report (results_comparem2/report_*.html) ?

As dbcan runs per sample, the directory is within samples/ The issue with eggnog (https://github.com/eggnogdb/eggnog-mapper/issues/571) is not relevant for dbcan, as dbcan is entirely independent of the eggnog output.

Thanks for your quick reply. Interesting approach but seems a bit indirect -- Is it not the purpose of Bactopia to be used to run genome-genome comparisons independently of assembly?