Configurations (Methods, TFs) of the benchmark can be defined in the config.yaml.
The workflow starts with downloading the ENCODE/GEO IDs of the preregistered datasets from the preregistered protocol on OSF. Subsequently, the specified data is downloaded from ENCODE/GEO and commonly preprocessed for all methods.
Currently methods are run based on local installs / conda environments. TODO:
- Separate docker containers for each method
- Push extra data required by methods to Zenodo to allow for downloads during Snakemake execution