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 and generate Pydantic models.
4. 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.
References	- See ../bio-skills-references.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
• 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.