To create the main conda environment, run mamba env create -f env.yaml.
After activating the environment and updating the config file, run workflow with:
snakemake --profile profiles/cluster . This will allow for cluster execution. Running snakemake --profile profiles/local will make the workflow run locally.
The organism is set in the config file under configs/config.yaml. Annotation files can be pointed to in the config as well, else they will be fetched from zenodo. Currently, mm10, mm39 and hg38 are supported.