I'm trying out snakemake 8. If have reason: True in a profile. I now get:

snakemake: error: unrecognized arguments: --reason=True

This isn't documented in the migration guide so it's either a bug or it should be added to the migration guide here: https://snakemake.readthedocs.io/en/stable/getting_started/migration.html#command-line-interface

Which currently reads:

Morever, some options have been renamed:

All the execution backends have been moved into plugins. When you used e.g. --kubernetes and corresponding options before, you should now use --executor kubeternes and check the Snakemake plugin catalog for the new options. The same holds for all other execution backends, see here.

The --use-conda and --use-singularity options are deprecated. Instead you should now use --software-deployment-method conda or --software-deployment-method apptainer or --software-deployment-method conda apptainer if you need both.

This seems to be the only breaking change, no other migration necessary for the nextstrain/mpox phylogenetic workflow, so not too bad ;)