- Update to snakemake 8.4
- Remove default configuration
- Update to snakemake 7.3
- Remove settings from the PEP configuration
- Switch to simplified PEP configuration (a csv is valid PEP)
- Reduce wait time for missing files to 5 seconds
- Keep temporary and failed files, to aid in debugging
- Add support for project configuration using PEP.
- Add integration tests using pytest-workflow and github workflows.