code: Remove unused inputs from snakefile

[euronion]

Seems like there are some unused input dependencies in the Snakefile that are no longer used. Historically grown and forgotten to be removed as code changed.

I went through only this file. Looks like something that can be semi-automated (flag + check). --> help wanted.

Note:
Sometimes dependencies are a bit hidden or inconsistent snakemake.input.file vs. snakemake.input["file"] vs. masking through function arguments inputs = snakemake.input and then inputs["file"].

Changes proposed in this Pull Request

Remove files from the input in the Snakefile that are no longer consumed by the scripts.

Checklist

• I tested my contribution locally and it works as intended.
• Code and workflow changes are sufficiently documented.
• Changed dependencies are added to pixi.toml (using pixi add <dependency-name>).
• Changes in configuration options are added in config/config.default.yaml.
• Changes in configuration options are documented in doc/configtables/*.csv.
• Sources of newly added data are documented in doc/data_sources.rst.
• A release note doc/release_notes.rst is added.