Update 24-11-12: The bug that was introduced in Snakemake 8.25.1 that caused bash scripts to fail has been fixed in 8.25.3, so versions of Snakemake >= 8.25.3 should work now.
Bug fix: explicitly set Snakemake version to 8.25.0 in the environment, which has been tested to be fully working with this workflow.
Full Changelog: v0.4.0...v0.4.1