chore: apply snakefmt

[corneliusroemer]

No description provided.

[victorlin]

I'm assuming you have local configuration since CI's snakefmt didn't detect anything prior to this PR. Can you push your configuration in a pyproject.toml file?

[corneliusroemer]

Ah, great point! I actually was confused that I needed to specify the folder explicitly and opened an issue snakemake/snakefmt#202

I don't know why this isn't recognized, is it nested too deep? I don't have a pyproject.toml, I had to manually run snakefmt on the file (I saw VS code complain, the plugin is great).

[corneliusroemer]

Ah, we're getting there:

$ snakefmt -vv .
...snip...
[DEBUG] Excluded: ingest/workflow/snakemake_rules/trigger_rebuild.smk matched the --exclude regular expression
...snip...

[corneliusroemer]

Ok this is why:

DEFAULT_EXCLUDES = (
    r"(\.snakemake|\.eggs|\.git|\.hg|\.mypy_cache|\.nox|\.tox|\.venv|\.svn|_build|"
    r"buck-out|build|dist|\.template)"
)

[victorlin]

Haha yeah, I realized at the same time and commented as snakemake/snakefmt#202 (comment).

[corneliusroemer]

This is a terrible exclude, it matches anything that contains build...

I suggest we start using this in our config: snakefmt -vv --exclude "" .