From 9 to 13 March 2026, about 40 developers, bioinformaticians, physicists, engineers and HPC experts gathered in Munich for the 2nd Snakemake Hackathon, supported by the U.S. National Science Foundation and BASF. Over five intensive days this community delivered numerous improvements, bug fixes, and new features that strengthen Snakemake's functionality and applicability.

Several of the advancements have been already released, while others will become available in the coming
Key advancements - illustrative rather than exhaustive - include:

• A refactored command-line interface which will introduce sub-commands to provide a better overview and functionality distinction
• Performance gains from bypassing DAG construction when unlocking directories
• An overhauled software deployment infrastructure
• An experimental SQLite‑backed metadata store that reduces file‑system pressure for massive workflows
• Improved handling of remote workflows hosted on Github or Gitlab as well as private deployments thereof
• Improved and restructured documentation
• Smarter and extended between workflow result caching
• Improvements for various executor plugins, most prominently SLURM (array jobs) and HTCondor (official maintenance transferred to HTCondor devs)
• Support for optional rule outputs and handling or tolerance for missing non-critical inputs
• Proof-of-concept WASM support for running lightweight workflows in the browser 

The hackathon demonstrates how Snakemake’s community‑driven development continues to strengthen reproducibility, scalability, and transparency for modern scientific computing.