bio-foundation-housekeepinglisted

# Bio Foundation Housekeeping Initialize a bioinformatics project scaffold with reproducible environments, schemas, and data cataloging. Use for new projects or repo setup. ## Instructions 1. Create standard directory layout (data/, results/, schemas/, workflows/, src/, notebooks/). 2. Initialize Pixi workspace and lockfile; define tasks. 3. Define LinkML schemas for sample, run, file, result, and provenance records. 4. Generate or hand-write Pydantic models from the LinkML schema and use them to parse/coerce incoming metadata before storage. 5. Validate raw records with LinkML/Pydantic, write normalized Parquet tables, then create the DuckDB catalog over validated Parquet only. ## Quick Reference | Task | Action | |------|--------| | Run workflow | Follow the steps in this skill and capture outputs. | | Validate inputs | Confirm required inputs and reference data exist. | | Review outputs | Inspect reports and QC gates before proceeding. | | Tool docs | See `docs/README.md`. | ## Input Requirements Prerequisites: - Tools available in the active environment (Pixi/conda/system). See `docs/README.md` for expected tools. - Target project root is writable. Inputs: - project root (path) - metadata schema requirements - workflow engine preference (optional) ## Output - pixi.toml - pixi.lock - schemas/ - data/catalog.duckdb - data/*.parquet validated against schemas/ - results/bio-foundation-housekeeping/report.md - results/bio-foundation-housekeeping/logs/ ## Quality Gate