The release of Snakemake 8 and 9 introduced breaking changes that forced HPC-dependent bioinformatics workflows to fundamentally rethink their cluster integration strategy — most notably, the removal of the long-standing `--cluster` flag in favor of a modern executor plugin interface. This talk walks through the real-world migration of DETECT, a simulation-based de novo mutation detection pipeline, from Snakemake 7 to Snakemake 9 on a SLURM HPC cluster. We cover the technical challenges encountered along the way: replacing inline cluster submission strings with the `snakemake-executor-plugin-slurm`, restructuring resource declarations into profile-based `set-resources` blocks, implementing automatic partition selection, and adding submission rate limiting to prevent SLURM socket timeouts at scale. Beyond the executor change, the migration prompted a broader modernization — containerizing GATK with Apptainer to eliminate conda instability, resolving Python environment path issues in shell rules, and building operational tooling for log analysis and interactive setup. Attendees will leave with a concrete migration roadmap and reusable patterns applicable to migrating from any Snakemake 7 workflow to Snakemake 8 and 9running on SLURM.
