Add JSON schema

[hoferand]

No description provided.

[sreichl]

Please address the comments and also run a test if it works (once with correct and once with not correctly filled config/annotation).

[hoferand]

incorporated feedback, tested, and still works

[hoferand]

really nice finding, I moved them and it still works 🎉 Thanks!

[sreichl]

ready to merge?

[hoferand]

yes

[sreichl]

@hoferand similarly to the formatting and linting, can you provide clear instructions and resources for setting up the validation scheme, including also but not limited to potential AI prompts that worked well? Thanks.

[hoferand]

Sure!

• Config Schemas
  • Create and use a schema for each config and annotation file, following the approach described in the Snakemake docs.
  • Place all schema files in workflow/schemas/ so they are easy to reference from the Snakefile.
  • Prompt used to generate the schemas (tested with Codex):

    Inspect the Snakemake workflow and identify every config or annotation field that is actually used. Create JSON Schema documents in YAML format under `workflow/schemas/` to match the real contract enforced by the workflow, not just the docs. Keep the schemas strict but simple, and prefer validator-compatible keywords. Update nearby documentation only if it helps future maintainers understand the validation setup. Use `https://json-schema.org/draft/2020-12/schema` for `$schema`.