bio-foundation-housekeeping
Installation
SKILL.md
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. |
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