I was surprised that snakemake files in subdirectories weren't included by default when running snakefmt .

In particular, the following directory and files were ignored when running from the project root:

root/
|-- workflow/
|   |-- snakemake_rules
|        |-- trigger_rebuild.smk
|        |-- upload.smk

I would expect that these files worfklow/snakemake_rules/trigger_rebuild.smk etc are included, because they match the default include regex .smk$