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 --cores 1 --use-envmodules . The workflow is currently configured to 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, only mm10 and hg38 are supported.