Bio Foundation Housekeeping
Initialize a bioinformatics project scaffold with reproducible environments, schemas, and data cataloging. Use for new projects or repo setup.
Instructions
- Create standard directory layout (data/, results/, schemas/, workflows/, src/, notebooks/).
- Initialize Pixi workspace and lockfile; define tasks.
- Define LinkML schemas and generate Pydantic models.
- Create DuckDB catalog and register parquet tables.
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.mdfor 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
- results/bio-foundation-housekeeping/report.md
- results/bio-foundation-housekeeping/logs/
Quality Gates
- Schema generation succeeds and models are importable.
- pixi.lock is created and consistent with pixi.toml.
- DuckDB catalog is readable.
- On failure: retry with alternative parameters; if still failing, record in report and exit non-zero.
- Verify project root exists and is writable.
- Validate generated schemas against expected fields.
Examples
Example 1: Expected input layout
project root (path)
metadata schema requirements
workflow engine preference (optional)Troubleshooting
Issue: Missing inputs or reference databases Solution: Verify paths and permissions before running the workflow.
Issue: Low-quality results or failed QC gates Solution: Review reports, adjust parameters, and re-run the affected step.