Common issues

Using singularity

If you forget the --use-singularity flag for Snakemake, you will find that many rules break due to the required tools not being available on your system.

Snakemake errors about reserved keywords

If you install Snakemake manually instead of using Conda and the provided environment.yml file, you might get errors about reserved keyword that are used in the Snakefiles. Please use the Snakemake version specified in the environment.yml file.